The women's singles of the 2006 ECM Prague Open tournament was played on clay in Prague, Czech Republic.

Dinara Safina was the defending champion, but competed in Berlin at the same week.

Shahar Pe'er won the title by defeating Samantha Stosur 4–6, 6–2, 6–1 in the final.

	Semifinals							Final
		Kaia Kanepi	3	0
	3	Shahar Pe'er	6	6
								3	Shahar Pe'er	4	6	6
								5	Samantha Stosur	6	2	1
	5	Samantha Stosur	6	6
	7	Peng Shuai	1	3

	First round							Second round							Quarterfinals							Semifinals
	1	M Bartoli	77	3	2
		K Kanepi	65	6	6				K Kanepi	7	1	710
		S Foretz	6	6					S Foretz	5	6	68
		E Gagliardi	3	3												K Kanepi	7	0	7
		V Kutuzova	2	2											6	ME Camerin	5	6	5
		M Shaughnessy	6	6					M Shaughnessy	5	4
		O Savchuk	4	1				6	ME Camerin	7	6
	6	ME Camerin	6	6																			K Kanepi	3	0
	3	S Pe'er	6	6																		3	S Pe'er	6	6
	WC	N Fraňková	3	1				3	S Pe'er	78	0	6
		Z Ondrášková	4	78	6				Z Ondrášková	66	6	3
		M Díaz Oliva	6	66	3										3	S Pe'er	7	6
		M Czink	1	6	6										8	A Bondarenko	5	0
		An Serra Zanetti	6	2	2				M Czink	6	0	2
		M Suchá	61	2				8	A Bondarenko	2	6	6
	8	A Bondarenko	77	6

	First round							Second round							Quarterfinals							Semifinals
	5	S Stosur	6	6
	Q	N Grandin	2	2				5	S Stosur	6	6
		A Morigami	6	6					A Morigami	1	2
	WC	B Strýcová	3	1											5	S Stosur	6	6
		A Harkleroad	6	4	3										4	É Loit	4	3
		K Šprem	0	6	6				K Šprem	4	3
	Q	A Radwańska	2	4				4	É Loit	6	6
	4	É Loit	6	6																		5	S Stosur	6	6
	7	S Peng	6	6																		7	S Peng	1	3
		B Mattek	2	3				7	S Peng	6	6
	Q	M Paštiková	6	7				Q	M Paštiková	2	4
	Q	V Azarenka	2	5											7	S Peng	7	6
		M Sequera	4	6	7										WC	M Rybáriková	5	4
		K Brandi	6	4	5				M Sequera	63	0
	WC	M Rybáriková	63	6	6			WC	M Rybáriková	77	6
	2	L Šafářová	77	4	4

• Main and Qualifying Draws