The knockout stage of the 2005–06 UEFA Cup began on 15 February 2006, and concluded with the final at the Philips Stadion in Eindhoven, Netherlands, on 10 May 2006. The final phase involved the 24 teams that finished in the top three in each group in the group stage and the eight teams that finished in third place in the UEFA Champions League group stage.
Each tie in the final phase, apart from the final, was played over two legs, with each team playing one leg at home. The team that had the higher aggregate score over the two legs progressed to the next round. In the event that aggregate scores finished level, the team that scored more goals away from home over the two legs progressed. If away goals are also equal, 30 minutes of extra time were played. If goals were scored during extra time and the aggregate score was still level, the visiting team qualified by virtue of more away goals scored. If no goals were scored during extra time, there would be a penalty shootout after extra time.
In the final, the tie was played over just one leg at a neutral venue. If scores were level at the end of normal time in the final, extra time was played, followed by penalties if scores had remained tied.
Seedings
In the draw for the Round of 32, matches were played between the winner of one group and the third-placed team of a different group, and between the runners-up of one group and the third-placed team from a Champions League group. The only restriction on the drawing of teams in the Round of 32 was that the teams must not be from the same national association or have played in the same group in the group stages. From the Round of 16 onwards, these restrictions did not apply.
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Bracket
Round of 32
The top three teams from each group were joined by the eight teams which finished third in their groups in the Champions League.
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg | 
|---|---|---|---|---|
| Litex Lovech  | 0–2 |  Strasbourg | 0–2 | 0–0 | 
| Stuttgart  | 2–2 (a) |  Middlesbrough | 1–2 | 1–0 | 
| Slavia Prague  | 2–2 (a) | .svg.png.webp) Palermo | 2–1 | 0–1 | 
| Heerenveen  | 2–3 |  Steaua București | 1–3 | 1–0 | 
| Lokomotiv Moscow  | 0–3 |  Sevilla | 0–1 | 0–2 | 
| Bolton Wanderers  | 1–2 |  Marseille | 0–0 | 1–2 | 
| Hertha BSC  | 0–3 |  Rapid București | 0–1 | 0–2 | 
| Basel .svg.png.webp) | 2–1 |  Monaco | 1–0 | 1–1 | 
| Udinese .svg.png.webp) | 3–1 |  Lens | 3–0 | 0–1 | 
| Rosenborg  | 1–4 |  Zenit Saint Petersburg | 0–2 | 1–2 | 
| Club Brugge .svg.png.webp) | 2–4 | .svg.png.webp) Roma | 1–2 | 1–2 | 
| Schalke 04  | 5–1 |  Espanyol | 2–1 | 3–0 | 
| Lille  | 3–2 |  Shakhtar Donetsk | 3–2 | 0–0 | 
| Thun .svg.png.webp) | 1–2 |  Hamburg | 1–0 | 0–2 | 
| Real Betis  | 3–2 |  AZ | 2–0 | 1–2(aet) | 
| Artmedia Bratislava  | 0–3 |  Levski Sofia | 0–1 | 0–2 | 
First leg
| Litex Lovech  | 0–2 |  Strasbourg | 
|---|---|---|
| Report | Le Pen  2' Diané  82' | 
| Stuttgart  | 1–2 |  Middlesbrough | 
|---|---|---|
| Ljuboja  86' | Report | Hasselbaink  20' Parnaby  46' | 
| Heerenveen  | 1–3 |  Steaua București | 
|---|---|---|
| Bruggink  24' | Report | Dică  29' Goian  76' Paraschiv  78' | 
| Lokomotiv Moscow  | 0–1 |  Sevilla | 
|---|---|---|
| Report | López  75' | 
| Hertha BSC  | 0–1 |  Rapid București | 
|---|---|---|
| Report | Negru  68' (pen.) | 
| Rosenborg  | 0–2 |  Zenit Saint Petersburg | 
|---|---|---|
| Report | Arshavin  22' Kerzhakov  32' | 
| Club Brugge .svg.png.webp) | 1–2 | .svg.png.webp) Roma | 
|---|---|---|
| Portillo  61' | Report | Vanaudenaerde  44' (o.g.) Perrotta  74' | 
| Lille  | 3–2 |  Shakhtar Donetsk | 
|---|---|---|
| Fauvergue  19' Dernis  57' Odemwingie  77' | Report | Brandão  89' Marica  90+1' | 
| Real Betis  | 2–0 |  AZ | 
|---|---|---|
| Tardelli  70' Robert  79' | Report | 
Second leg
Strasbourg won 2–0 on aggregate.
| Middlesbrough  | 0–1 |  Stuttgart | 
|---|---|---|
| Report | Tiffert  13' | 
2–2 on aggregate. Middlesbrough won on away goals.
| Palermo .svg.png.webp) | 1–0 |  Slavia Prague | 
|---|---|---|
| Godeas  51' | Report | 
2–2 on aggregate. Palermo won on away goals.
| Steaua București  | 0–1 |  Heerenveen | 
|---|---|---|
| Report | Bruggink  85' | 
Steaua București won 3–2 on aggregate.
| Sevilla  | 2–0 |  Lokomotiv Moscow | 
|---|---|---|
| Maresca  34' Puerta  90' | Report | 
Sevilla won 3–0 on aggregate.
| Marseille  | 2–1 |  Bolton Wanderers | 
|---|---|---|
| Ribéry  45+2' Ben Haim  68' (o.g.) | Report | Giannakopoulos  25' | 
Marseille won 2–1 on aggregate.
| Rapid București  | 2–0 |  Hertha BSC | 
|---|---|---|
| Niculae  50' Buga  79' | Report | 
Rapid București won 3–0 on aggregate.
Basel won 2–1 on aggregate.
Udinese won 3–1 on aggregate.
Zenit Saint Petersburg won 4–1 on aggregate.
Roma won 4–2 on aggregate.
Schalke 04 won 5–1 on aggregate.
Lille won 3–2 on aggregate.
| Hamburg  | 2–0 | .svg.png.webp) Thun | 
|---|---|---|
| Van Buyten  2', 33' | Report | 
Hamburg won 2–1 on aggregate.
Real Betis won 3–2 on aggregate.
| Levski Sofia  | 2–0 |  Artmedia Bratislava | 
|---|---|---|
| Angelov  14', 27' | Report | 
Levski Sofia won 3–0 on aggregate.
Round of 16
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg | 
|---|---|---|---|---|
| Rapid București  | 3–3 (a) |  Hamburg | 2–0 | 1–3 | 
| Basel .svg.png.webp) | 4–2 |  Strasbourg | 2–0 | 2–2 | 
| Middlesbrough  | 2–2 (a) | .svg.png.webp) Roma | 1–0 | 1–2 | 
| Steaua București  | 3–0 |  Real Betis | 0–0 | 3–0 | 
| Palermo .svg.png.webp) | 1–3 |  Schalke 04 | 1–0 | 0–3 | 
| Marseille  | 1–2 |  Zenit Saint Petersburg | 0–1 | 1–1 | 
| Udinese .svg.png.webp) | 1–2 |  Levski Sofia | 0–0 | 1–2 | 
| Lille  | 1–2 |  Sevilla | 1–0 | 0–2 | 
First leg
| Rapid București  | 2–0 |  Hamburg | 
|---|---|---|
| Niculae  45+2' Buga  88' | Report | 
| Basel .svg.png.webp) | 2–0 |  Strasbourg | 
|---|---|---|
| Delgado  86' Kuzmanović  89' | Report | 
| Middlesbrough  | 1–0 | .svg.png.webp) Roma | 
|---|---|---|
| Yakubu  12' (pen.) | Report | 
| Palermo .svg.png.webp) | 1–0 |  Schalke 04 | 
|---|---|---|
| Brienza  15' | Report | 
Second leg
| Hamburg  | 3–1 |  Rapid București | 
|---|---|---|
| Lauth  24' Barbarez  36' Van der Vaart  62' | Report | Buga  51' | 
3–3 on aggregate, Rapid București won on away goals.
Basel won 4–2 on aggregate.
| Roma .svg.png.webp) | 2–1 |  Middlesbrough | 
|---|---|---|
| Mancini  43', 66' (pen.) | Report | Hasselbaink  32' | 
2–2 on aggregate, Middlesbrough won on away goals.
| Real Betis  | 0–3 |  Steaua București | 
|---|---|---|
| Report | Nicoliță  54', 82' Iacob  78' | 
Steaua București won 3–0 on aggregate.
| Schalke 04  | 3–0 | .svg.png.webp) Palermo | 
|---|---|---|
| Kobiashvili  44' (pen.) Larsen  72' Azaouagh  80' | Report | 
Schalke 04 won 3–1 on aggregate.
| Zenit Saint Petersburg  | 1–1 |  Marseille | 
|---|---|---|
| Kerzhakov  69' | Report | Déhu  74' | 
Zenit Saint Petersburg won 2–1 on aggregate.
Levski Sofia won 2–1 on aggregate.
| Sevilla  | 2–0 |  Lille | 
|---|---|---|
| Kanouté  29' Luís Fabiano  45+2' | Report | 
Sevilla won 2–1 on aggregate.
Quarter-finals
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg | 
|---|---|---|---|---|
| Sevilla  | 5–2 |  Zenit Saint Petersburg | 4–1 | 1–1 | 
| Basel .svg.png.webp) | 3–4 |  Middlesbrough | 2–0 | 1–4 | 
| Rapid București  | 1–1 (a) |  Steaua București | 1–1 | 0–0 | 
| Levski Sofia  | 2–4 |  Schalke 04 | 1–3 | 1–1 | 
First leg
| Basel .svg.png.webp) | 2–0 |  Middlesbrough | 
|---|---|---|
| Delgado  43' Degen  45+1' | Report | 
| Rapid București  | 1–1 |  Steaua București | 
|---|---|---|
| Moldovan  50' | Report | Nicoliță  5' | 
| Levski Sofia  | 1–3 |  Schalke 04 | 
|---|---|---|
| Borimirov  6' | Report | Varela  48' Lincoln  69' Asamoah  79' | 
Second leg
| Zenit Saint Petersburg  | 1–1 |  Sevilla | 
|---|---|---|
| Hyun  50' | Report | Kepa  66' | 
Sevilla won 5–2 on aggregate.
| Middlesbrough  | 4–1 | .svg.png.webp) Basel | 
|---|---|---|
| Viduka  33', 57' Hasselbaink  79' Maccarone  90' | Report | Eduardo  23' | 
Middlesbrough won 4–3 on aggregate.
1–1 on aggregate. Steaua București won on away goals.
| Schalke 04  | 1–1 |  Levski Sofia | 
|---|---|---|
| Lincoln  58' | Report | Angelov  24' | 
Schalke 04 won 4–2 on aggregate.
Semi-finals
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg | 
|---|---|---|---|---|
| Schalke 04  | 0–1 |  Sevilla | 0–0 | 0–1 (aet) | 
| Steaua București  | 3–4 |  Middlesbrough | 1–0 | 2–4 | 
First leg
| Schalke 04  | 0–0 |  Sevilla | 
|---|---|---|
| Report | 
| Steaua București  | 1–0 |  Middlesbrough | 
|---|---|---|
| Dică  30' | Report | 
Second leg
| Sevilla  | 1–0 (a.e.t.) |  Schalke 04 | 
|---|---|---|
| Puerta  101' | Report | 
Sevilla won 1–0 on aggregate.
| Middlesbrough  | 4–2 |  Steaua București | 
|---|---|---|
| Maccarone  33', 89' Viduka  64' Riggott  73' | Report | Dică  16' Goian  24' | 
Middlesbrough won 4–3 on aggregate.
Final
| Middlesbrough  | 0–4 |  Sevilla | 
|---|---|---|
| Report | Luís Fabiano  27' Maresca  78', 84' Kanouté  89' |