They had their first official international match as a 4–1 victory against Slovenia in a friendly on 13 October 1993 under coach Andon Dončevski.^[5] In 1994, the newly proclaimed Republic of Macedonia became a separate member of FIFA and UEFA after its independence referendum and split of the Yugoslav federal team.

The UEFA Euro 1996 qualifying was the first major qualifying tournament that Macedonia participated in as an independent nation, grouped with Spain, Denmark, Belgium, Cyprus and Armenia. In their opening game, which was also their first ever official match, Macedonia played the reigning European champions Denmark, finishing 1–1 after Macedonia led for most of the game.^[6] Later, Macedonia suffered one of its worst ever defeats, 5–0 against Belgium on 7 June 1995.^[7] They failed to qualify for UEFA Euro 1996, finishing fourth in the group with seven points.^[8]

The tournament began on 24 April 1996 with a 3–0 win at home against Liechtenstein. On 9 November 1996, Macedonia recorded their biggest ever, an 11–1 thrashing victory against Liechtenstein.^[9] Macedonia defeated the Republic of Ireland 3–2 at home, their first victory against a major European team, but failed again to qualify for the 1998 World Cup in France, finishing fourth in the group on 13 points.^[10]

Macedonia's journey to qualify for the UEFA Euro 2000 in the Netherlands and Belgium saw them grouped with FRY, Republic of Ireland, Croatia, and Malta. They once again opened their qualifying campaign with a victory after beating Malta 4–0 at home on 6 September 1998. Their most notable result in the campaign was a 1–1 draw against Croatia in June 1999, with an equalizer of Georgi Hristov ten minutes before the end of the game. They helped Yugoslavia qualify directly and eliminate Croatia because they drew 1–1 against the Republic of Ireland with a last-minute equalizer of Goran Stavrevski. However, they failed to qualify again, finishing fourth in the group with eight points.^[11]

Macedonia's 2002 World Cup qualifying campaign saw them grouped with Sweden, Turkey, Slovakia, Moldova, and Azerbaijan. They were unsuccessful in their opening match, going down to Slovakia 2–0 in Bratislava on 3 September 2000. The Macedonians once again failed to qualify for the 2002 World Cup as they finished fourth in the group with seven points.^[12]

The Euro 2004 Qualifiers saw Macedonia grouped alongside England, Turkey, Slovakia, and Liechtenstein. Macedonia played England in Southampton, England's first home match in Southampton in almost 100 years. Macedonia grabbed the lead early in the first half after Artim Šakiri scored directly from a corner kick. England soon leveled the game, before Macedonia led again. The game eventually ended 2–2.^[13] Macedonia lost to England 2–1 at home in the return leg, which took place in September 2003.^[14] Macedonia's only win of the campaign came on 7 June 2003, when they beat Liechtenstein 3–1 at home.

On 9 October 2004, Macedonia managed to hold the Netherlands to a surprise 2–2 draw in Skopje in front of a crowd of 17,000 at the Skopje City Stadium,^[15] but just four days later, they suffered a 1–0 loss away to Andorra.^[16] Macedonia then set a new team record for most goals conceded in a game when they lost 6–1 away to the Czech Republic in June 2005.

Macedonia opened its UEFA Euro 2008 qualifying campaign with a 1–0 away victory against Estonia on 16 August 2006. Macedonia hosted England on 6 September in their second game of the qualifiers. England went on to win 1–0, the first time that Macedonia failed to score against the country.^[17]

A month later, on 7 October 2006, the two teams met once again in Manchester, where England was held to a 0–0 draw in front of 72,062 people.^[18] On 17 October 2007, Macedonia recorded their first win on home soil since August 2004 when they defeated Andorra 3–0 in Skopje.^[19]

Macedonia then recorded one of their most impressive wins to date when they picked up a 2–0 victory over eventual group winners Croatia on 17 November 2007. It was also a first victory for Macedonia against a nation that was ranked in the top ten of the FIFA World Rankings.^[20] Despite this, Macedonia failed to qualify for Euro 2008 after finishing fifth in the group with 14 points.^[21]

On 25 November 2007, just days after Macedonia completed its qualifying campaign for Euro 2008, the groups for European qualifiers for the 2010 World Cup were held in Durban, South Africa, where Macedonia was seeded in Pot 4 and grouped along with the Netherlands, Scotland, Norway and Iceland.^[22] Manager Srečko Katanec received a two-year extension on 21 December 2007, which meant he would be under contract through the end of the 2010 World Cup qualifiers.^[23] In the lead up to the campaign, Macedonia played three friendlies against Serbia, Bosnia and Herzegovina and Poland, which all ended in draws.

On 6 September 2008, Macedonia opened their campaign with a 1–0 home win against Scotland when Ilčo Naumoski scored on a rebound after a missed free kick by Goce Sedloski. Following these impressive results, they moved up ten places to 46th in the FIFA world rankings for October 2008, their highest ever ranking. However, Katanec resigned following a 4–0 loss to the Netherlands in Amsterdam in April 2009, allegedly for getting into an argument with Goran Pandev.^[24]

Soon afterwards, the manager of the under-21 team, Mirsad Jonuz, was appointed senior coach and remained until the end of the World Cup qualifying campaign.^[25] On 12 August 2009, a friendly match against Spain was held at the newly built City Park Stadium in Skopje. The defending European champions won 3–2 after being 2–0 down at halftime.^[26] In September, Macedonia lost 2–0 against Scotland and Norway.

Macedonia was placed in Group B for the Euro 2012 qualifiers alongside Russia, Slovakia, Republic of Ireland, Armenia and Andorra.^[27] In the lead up to the qualifiers, an under-strength Macedonia side played friendlies against Azerbaijan, Romania, and Malta, winning the first two 3–1 and 1–0 respectively, and tied 1–1 against Malta later the summer.

Macedonia finished fifth in the group with only two victories against Andorra as well as two home draws, against Armenia and Slovakia. Coach Mirsad Jonuz was dismissed on 18 June 2011^[28] and replaced by John Toshack.^[29]

Macedonia's 2014 World Cup qualifying campaign saw them grouped with Croatia, Serbia, Belgium, Scotland and Wales.^[30] In August 2012, prior to the qualifiers, John Toshack resigned^[31] and was replaced by Čedomir Janevski.^[32] The national team would begin the qualification round with a loss to Croatia in Zagreb and would go on to draw against Scotland in Glasgow. They lost again to Croatia and won against Serbia in Skopje after a penalty kick taken by Agim Ibraimi.^[33] Later in qualification, the national team would go on to lose twice to the eventual group winners Belgium.

Macedonia would beat Wales and lose against Scotland at home. Around the end of September 2013, Janevski would leave the team for Belgian club R.A.E.C. Mons^[34] and would be replaced by Zoran Stratev for the last two matches.^[35] Away losses to Wales and Serbia meant they would finish last in their group.

After the run, Goran Pandev, Nikolče Noveski, Veliče Šumulikoski and others would retire from the national team due to turbulent relations with the Football Federation of Macedonia.^[36] In November 2013, Boško Gjurovski would be appointed the new national team manager.^[37]

Ironically, a significant number of players originally from Macedonia appeared at the 2014 World Cup, including Blerim Džemaili, Admir Mehmedi and Shkodran Mustafi who couldn't be convinced to represent Macedonia instead.

On 23 February 2014, Macedonia was placed in Group C for the Euro 2016 qualifiers alongside Spain, Ukraine, Slovakia, Belarus and Luxembourg.^[38] With 5–1 loss against Spain in Valencia, the only victory they earned was against Luxembourg in Skopje.

After four losses, coach Boško Gjurovski was dismissed on 7 April 2015^[39] and replaced by Ljubinko Drulović.^[40] Further losses came against Slovakia and surprisingly Luxembourg. Macedonia drew their last match with Belarus in Barysaw, but still finished last in their group.

On 25 July 2015, in the middle of the Euro 2016 qualifying, Macedonia was seeded in Pot 5. They were put in the same group as Spain again, for the first time with Italy, along with Albania , Israel, and Liechtenstein.^[41]

In October 2015, Drulović left the national team.^[42] and the manager place was taken over by the former manager of Rabotnički, Igor Angelovski.^[43] That same month, 2010 UEFA Champions League champion Goran Pandev came back to the national team after two years of absence.^[44]

Macedonia started with another disappointing loss against Albania in Shkodër, with a goal scored by Bekim Balaj in the last moments of the game, in a match that was played over two days because of interruption in the 76th minute due to weather.^[45][46] Later on they also lost to Israel at home after missing a penalty kick by Adis Jahović.^[47] After that, the national team also lost to Italy beside their 2–1 lead with the goals scored by Ilija Nestorovski and Ferhan Hasani.^[48] At the end of 2016, Macedonia was beaten by Spain in Granada 4–0;^[49] Macedonia had not scored a single point, the worst qualifying start in the history of the national team.^[50]

In March 2017, Macedonia recorded their first 3–0 qualification victory against Liechtenstein.^[51] They later lost against Spain in Skopje 2–1.^[52] Macedonia also defeated Israel away through the sole goal by Goran Pandev, which was also a first ever victory against Israel.^[53] Macedonia later tied Albania in Strumica 1–1.^[54]

In the inaugural UEFA Nations League, Macedonia played in League D, the lowest division.^[55] Macedonia were drawn in Group 4 with Armenia, Liechtenstein and Gibraltar.^[56] The national team won the group with five wins and one loss, were promoted to the League C for the next edition of the Nations League, and were assured of a UEFA Euro 2020 qualifying play-offs place.^[57]

For the UEFA Euro 2020 qualifying, the newly-renamed North Macedonia were placed in Group G, along with Austria, Israel, Latvia, Poland, and Slovenia.^[58] North Macedonia managed two first impressive results with a 1–1 away draw against Slovenia.^[59] Prior to the match, Macedonia defeated Latvia 3–1 at home,.^[60] However, North Macedonia would soon fall 1–0 to Poland^[61] and 4–1 to Austria.^[62] Later, the North Macedonia recorded a 1–1 away draw against Israel,^[63] and a 2–1 home victory against Slovenia.^[64] North Macedonia lost 2–0 away against Poland,^[65] and 2–1 away against Austria, ending up in third place.^[66]

However, due to them having successfully taken first place in the UEFA Nations League earlier, North Macedonia eventually reached its first ever competitive playoff in history and was scheduled against Kosovo. Eventually, in the UEFA Euro 2020 qualifying play-offs semi-final, North Macedonia overcame Kosovo 2–1 at home. Then they faced Georgia in the final of Path D's play-offs on 13 November in Tbilisi, winning 1–0.^[67]

After winning the League D group in the first edition of the UEFA Nations League, North Macedonia were promoted to the third division of the competition, League C. North Macedonia was drawn in Group 2 together with Armenia, Estonia and Georgia.^[68]

North Macedonia made their Euros debut in 2020, postponed to 2021 due to the COVID-19 pandemic. All three Group C matches ended up in a loss, to Austria, Ukraine, and the Netherlands; Goran Pandev equalized against Austria in the 28th minute and Ezgjan Alioski scored against Ukraine. North Macedonia was the second debutant, after Finland.

For the 2022 World Cup qualifying campaign, North Macedonia was drawn in Group J with Germany, Romania, Iceland, Armenia and Liechtenstein.^[69] On matchday 3, North Macedonia inflicted a 2–1 defeat on Germany in Duisburg, which was Germany's first World Cup qualification defeat since 2001 and only the third in their history.^[70][71] In the last two games against Armenia and Iceland, North Macedonia won both (5–0 away against Armenia, 3–1 against Iceland) to put them in 2nd in Group J. Qualifying for the play-offs, they defeated reigning European champions Italy in Palermo on 24 March 2022, and faced Portugal in the play-off final on 29 March where they lost 2–0.^[72][73]

North Macedonia played in the UEFA Nations League against Georgia, Gibraltar, and Bulgaria – eventually finishing third place. Meanwhile, in the UEFA Euro 2024 qualifying, North Macedonia failed to qualify for the UEFA Euro 2024, finishing fourth in their group after England, Italy, Ukraine, and above Malta.^[74]