The knockout stage of the 2006–07 UEFA Cup began on 14 February 2007, culminating with the final at Hampden Park, Glasgow, on 16 May 2007. The knockout stage included the top three teams from each group in the previous stage and the third-placed teams from the 2006–07 UEFA Champions League group stage.

Each knockout round tie consisted of two-legged matches, home and away, in which the team with the higher aggregate score progressed to the next round, with the exception of the final, which was played over just one match at a neutral venue. In the event that the two teams' aggregate scores were tied, the team that scored more goals in their away leg would progress to the next round.

Bracket

	Round of 32						Round of 16						Quarter-finals						Semi-finals						Final
	CSKA Moscow	0	0	0
	Maccabi Haifa	0	1	1			Maccabi Haifa	0	0	0
	Livorno	1	0	1			Espanyol	0	4	4
	Espanyol	2	2	4									Espanyol	3	0	3
	AEK Athens	0	0	0									Benfica	2	0	2
	Paris Saint-Germain	2	2	4			Paris Saint-Germain	2	1	3
	Benfica	1	2	3			Benfica	1	3	4
	Dinamo București	0	1	1															Espanyol	3	2	5
	Zulte Waregem	1	0	1															Werder Bremen	0	1	1
	Newcastle United	3	1	4			Newcastle United	4	0	4
	Fenerbahçe	3	2	5			AZ ( a)	2	2	4
	AZ ( a)	3	2	5									AZ	0	1	1
	Spartak Moscow	1	1	2									Werder Bremen	0	4	4
	Celta Vigo	1	2	3			Celta Vigo	0	0	0
	Werder Bremen	3	1	4			Werder Bremen	1	2	3
	Ajax	0	3	3																					Espanyol	2 (1)
	Lens	3	0	3																					Sevilla ( p)	2 (3)
	Panathinaikos	1	0	1			Lens	2	0	2
	Bayer Leverkusen	3	0	3			Bayer Leverkusen	0	3	3
	Blackburn Rovers	2	0	2									Bayer Leverkusen	0	0	0
	Hapoel Tel Aviv	2	0	2									Osasuna	3	1	4
	Rangers	1	4	5			Rangers	1	0	1
	Bordeaux	0	0	0			Osasuna	1	1	2
	Osasuna	0	1	1															Osasuna	1	0	1
	Steaua București	0	0	0															Sevilla	0	2	2
	Sevilla	2	1	3			Sevilla	2	3	5
	Shakhtar Donetsk	1	1	2			Shakhtar Donetsk	2	2	4
	Nancy	1	0	1									Sevilla	2	2	4
	Braga	1	1	2									Tottenham Hotspur	1	2	3
	Parma	0	0	0			Braga	2	2	4
	Feyenoord	–	–	–			Tottenham Hotspur	3	3	6
	Tottenham Hotspur ( w/o)	–	–	–

Round of 32

On 7 February, the Italian government ruled Parma and Livorno's home fields did not meet safety requirements following riots that occurred after a Serie A match in Sicily. Both sides played their home legs behind closed doors.

On 19 January, UEFA declared that Feyenoord had been removed after crowd misbehaviour in their final group stage match against Nancy; UEFA announced on 25 January that their scheduled opponents, Tottenham Hotspur, had received a bye. Feyenoord unsuccessfully appealed the decision.

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Zulte Waregem	1–4	Newcastle United	1–3	0–1
Braga	2–0	Parma1	1–0	1–0
Lens	3–1	Panathinaikos	3–1	0–0
Bayer Leverkusen	3–2	Blackburn Rovers	3–2	0–0
Hapoel Tel Aviv	2–5	Rangers	2–1	0–4
Livorno1	1–4	Espanyol	1–2	0–2
Feyenoord2	(w/o)	Tottenham Hotspur	–	–
Fenerbahçe	5–5 ( a)	AZ	3–3	2–2
Werder Bremen	4–3	Ajax	3–0	1–3
Spartak Moscow	2–3	Celta Vigo	1–1	1–2
CSKA Moscow	0–1	Maccabi Haifa	0–0	0–1
AEK Athens	0–4	Paris Saint-Germain	0–2	0–2
Benfica	3–1	Dinamo București	1–0	2–1
Steaua București	0–3	Sevilla	0–2	0–1
Shakhtar Donetsk	2–1	Nancy	1–1	1–0
Bordeaux	0–1	Osasuna	0–0	0–1 ( a.e.t.)

First leg

All times CET

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Second leg

All times CET

AZ won on away goals. The aggregate score was 5–5.

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Maccabi Haifa won 1–0 on aggregate.

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Bayer Leverkusen won 3–2 on aggregate.

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Shakhtar Donetsk won 2–1 on aggregate.

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Benfica won 3–1 on aggregate.

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Celta Vigo won 3–2 on aggregate.

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Newcastle United won 4–1 on aggregate.

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Osasuna won 1–0 on aggregate.

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Lens won 3–1 on aggregate.

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Paris Saint-Germain won 4–0 on aggregate.

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Braga won 2–0 on aggregate.

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Sevilla won 3–0 on aggregate.

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Werder Bremen won 4–3 on aggregate.

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Rangers won 5–2 on aggregate.

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Espanyol won 4–1 on aggregate.

Bye: Tottenham Hotspur

Notes

• Note 1: Maccabi Haifa played their home matches at Bloomfield Stadium in Tel Aviv instead of their regular stadium, Kiryat Eliezer Stadium, Haifa.

Round of 16

The first legs were played on 8 March 2007, while the second legs were played on 14 and 15 March 2007.

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Newcastle United	4–4 ( a)	AZ	4–2	0–2
Maccabi Haifa	0–4	Espanyol	0–0	0–4
Rangers	1–2	Osasuna	1–1	0–1
Braga	4–6	Tottenham Hotspur	2–3	2–3
Sevilla	5–4	Shakhtar Donetsk	2–2	3–2 ( a.e.t.)
Lens	2–4	Bayer Leverkusen	2–1	0–3
Paris Saint-Germain	3–4	Benfica	2–1	1–3
Celta Vigo	0–3	Werder Bremen	0–1	0–2

First leg

All times CET

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Second leg

All times CET

Bayer Leverkusen won 4–2 on aggregate.

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Osasuna won 2–1 on aggregate.

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Werder Bremen won 3–0 on aggregate.

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Tottenham Hotspur won 6–4 on aggregate.

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Sevilla won 5–4 on aggregate.

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AZ won on away goals. The aggregate score was 4–4.

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Espanyol won 4–0 on aggregate.

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Benfica won 4–3 on aggregate.

Notes

• Note 1: Maccabi Haifa played their home matches at Bloomfield Stadium in Tel Aviv instead of their regular stadium, Kiryat Eliezer Stadium, Haifa.

Quarter-finals

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
AZ	1–4	Werder Bremen	0–0	1–4
Bayer Leverkusen	0–4	Osasuna	0–3	0–1
Sevilla	4–3	Tottenham Hotspur	2–1	2–2
Espanyol	3–2	Benfica	3–2	0–0

First leg

All times CET

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Second leg

All times CET

Espanyol won 3–2 on aggregate.

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Osasuna won 4–0 on aggregate.

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Sevilla won 4–3 on aggregate.

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Werder Bremen won 4–1 on aggregate.

Semi-finals

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Espanyol	5–1	Werder Bremen	3–0	2–1
Osasuna	1–2	Sevilla	1–0	0–2

First leg

All times CET

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Second leg

All times CET

Sevilla won 2–1 on aggregate.

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Espanyol won 5–1 on aggregate.

Final