The 2016–17 EHF Challenge Cup was the 20th edition of the European Handball Federation's third-tier competition for men's handball clubs, which was won by Sporting CP running from 19 November 2016 to 27 May 2017.

• TH: Title holders

Round 3
HC Visé BM	RK Vogošća Poljine Hills	HC Lokomotiv Varna	HC Dobrudja
A.S.S. Spes	Cambridge HC	A.C. Doukas	IEK Xini Dikeas
Valur	Hapoel Ashdod	Ramat Hashron "S.G.S." HC	A.S.D. Romagna Handball
KH Kastrioti	Klaipeda Dragunas	Handball Esch	HB Dudelange
PGU-Kartina TV Tiraspol	Riviera-SSSH-2	RK Pelister	RK Partizan 1949
JMS Hurry-Up	Haslum Handballklubb	Sporting CP	AHC Potaissa Turda
RK Sloga Požega	RK Partizan	TSV St. Otmar St. Gallen	HKM Sala
MSK Povazska Bystrica	Göztepe SK	Tasova Yibo SK	HC ZNTU-ZAB Zaporizhzhia

All draws held at the European Handball Federation headquarters in Vienna, Austria.

Teams listed first played the first leg at home. Some teams agreed to play both matches in the same venue. Bolded teams qualified into last 16.

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Sporting CP	69–49	A.S.D. Romagna Handball	32–25	37–24
AHC Potaissa Turda	75–42	HC Dobrudja	32–23	43–19
HB Dudelange	56–55	Hapoel Ashdod	23–28	33–27
RK Sloga Požega	50–47	HC Visé BM	26–21	24–26
PGU-Kartina TV Tiraspol	51–58	HC ZNTU-ZAB Zaporizhzhia	23–27	28–31
Ramat Hashron "S.G.S." HC	39–54	Handball Esch	21–29	18–25
RK Partizan 1949	49–43	A.S.S. Spes	27–21	22–22
RK Partizan	52–59	MSK Povazska Bystrica	23–31	29–28
Valur	56–49	Haslum Handballklubb	31–24	25–25
IEK Xini Dikeas	43–45	A.C. Doukas	27–21	16–24
KH Kastrioti	51–60	HKM Sala	29–31	22–29
Göztepe SK	47–48	JMS Hurry-Up	22–20	25–28
Klaipeda Dragunas	52–63	TSV St. Otmar St. Gallen	28–35	24–28
Tasova Yibo SK	65–56	Riviera-SSSH-2	32–29	33–27
Cambridge HC	47–76	HC Lokomotiv Varna	22–36	25–40
RK Pelister	49–48	RK Vogošća Poljine Hills	21–23	28–25

Teams listed first played the first leg at home. Some teams agreed to play both matches in the same venue. Bolded teams qualified into quarter-finals.

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Tasova Yibo SK	58–66	A.C. Doukas	28–32	30–34
Valur	45–45	RK Partizan 1949	21–21	24–24
Handball Esch	56–59	AHC Potaissa Turda	27–31	29–28
HC ZNTU-ZAB Zaporizhzhia	54–57	HB Dudelange	27–32	27–25
HKM Sala	57–55	TSV St. Otmar St. Gallen	30–27	27–28
RK Pelister	44–66	Sporting CP	18–32	26–34
MSK Povazska Bystrica	49–51	JMS Hurry-Up	30–19	19–32
RK Sloga Požega	58–44	HC Lokomotiv Varna	35–22	23–22

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
RK Sloga Požega	53–59	Valur	27–30	26–29
AHC Potaissa Turda	68–64	HB Dudelange	32–29	36–35
A.C. Doukas	48–62	Sporting CP	23–35	25–27
JMS Hurry-Up	66–56	HKM Sala	28–24	38–32

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
JMS Hurry-Up	41–69	Sporting CP	27–32	14–37
Valur	53–54	AHC Potaissa Turda	30–22	23–32

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Sporting CP	67–52	AHC Potaissa Turda	37–28	30–24

• 2016–17 EHF Champions League
• 2016–17 EHF Cup

• EHF Challenge Cup (official website)