The 2005–06 season was Fussball Club Basel 1893's 113th in existence and the club's 12th consecutive season in the top flight of Swiss football. Werner Edelmann was confirmed as the club's chairman for the fourth successive season at the AGM. FCB played their home matches in the St. Jakob-Park, in the Basel quarter St. Alban in the south-east of the city.

Overview Christian Gross was head coach for the seventh successive season. A number of players left the squad. Marco Zwyssig retired from active football. Sébastien Barberis was released on a free transfer, after eight years with the club and he moved on to FC Bulle. Philipp Degen transferred to Borussia Dortmund and Benjamin Huggel transferred to Eintracht Frankfurt. Goalkeeper Thomas Mandl returned to Austria and signed for Admira Wacker Mödling and defender Kléber returned to Brazil, signing for Santos. The two Argentinian strikers Christian Giménez and Julio Hernán Rossi also left the club, Giménez in August and Rossi during the winter break. Giménez parting was somewhat peculiar, he forced his immediate departure to the French team Olympique de Marseille by refusing to play against Werder Bremen.

Basel made a few signings before the start of the 2005–06 season. For example, forward Eduardo, who was signed permanently from Toulouse, following his successful loan spell. The young forward Felipe Caicedo was signed in from Rocafuerte Fútbol Club. Midfielders Baykal Kulaksızoğlu was signed in from FC Thun and Papa Malick Ba from CS Sfaxien, goalkeeper Louis Crayton was signed in from Concordia Basel and a number of youngsters advanced from the U-21 team including Ivan Rakitić and Zdravko Kuzmanović.

The FC Basel aims for the 2005–06 season were to retain the league title, win the cup and as well as to qualify for the UEFA Champions League group stage.

FC Basel started the season with various warm-up matches. These included teams from the Swiss lower league as well as teams from France, Croatia and Ukraine. They played six pre-season friendlies including the Uhrencup in Grenchen, winning four matches, but losing in the Uhrencup 0–2 against 1. FC Kaiserslautern and drawing the second match in this competition 2–2 against Trabzonspor. The six mid-season friendlies all ended with a victory.

During the winter break, the team had their traditional winter break soccer camp in La Manga, Spain. The defenders Daniel Majstorović and Kōji Nakata were brought in to replace Lyon-bound Patrick Müller and Murat Yakın who was to retire at the end of the season. The team played two games in their soccer camp, drawing 2–2 against German team Hamburger SV and beat local team Ciudad de Murcia 2–1. The other three winter break matches were played in Switzerland. Basel beat Locarno and beat Wohlen, bur lost against Rapid București. Of their 17 friendlies in this season, Basel won 13 matches, drew two and lost two.

The Campaign Domestic league There were ten teams competing in the top tier 2005–06 Swiss Super League. The teams played a double round-robin in the first half of the season and then another double round-robin in the second half. There were three points for a victory and one each for a draw. The champions would enter the second qualifying round of the 2006–07 UEFA Champions League. The championship runners-up and the third placed team would enter the UEFA Cup first qualifying round. The bottom placed team would be relegated, the second last team would play a play-off against relegation.

Basel's priority aim for the season was to win the league championship for the third time in a row. Despite the 3–0 defeat by FC Thun in the second round, Basel started the season well and led the championship right until the last day of the league campaign. On 26 February 2006, FC Basel broke their own club record of 52 unbeaten league games at St. Jakob Park, later extending it to 59. The unbeaten home run ended on the final day of the season with a last-minute goal from Zürich's Iulian Filipescu giving Zürich their first national championship since 1980–81. A 60th straight home league match undefeated, would have made Basel champions for third time in a row. The final score was 1–2 in favour of Zürich. The title was lost on goal difference.

The last minute loss of the Championship and the subsequent riots, the so-called Basel Hooligan Incident, meant that the club would suffer the consequences. As well as a huge fine, the first two home games of their 2006–07 season were held completely without fans, behind closer doors. The following three matches were held with just a part of the stadium capacity, without the fans from the "Muttenzer Kurve" (the eastern fan block).

Domestic cup Basel's clear aim for the Swiss Cup was to win it. In the first round of the 2005–06 Cup Basel were drawn away against lower league team Solothurn. Basel won this 4–1, with goals from David Degen, and Eduardo and twice Mladen Petrić. In round two they were drawn away against local lower league team Old Boys. Basel won this 6–1 and here Mile Sterjovski scored four goals and Zdravko Kuzmanović scored the other two. However, despite an early goal from Julio Hernán Rossi and two further goals from Matías Delgado, Basel were defeated in the third round home tie against FC Zürich 3–4. Basel's domestic cup aim was clearly missed. Second tier Sion won the trophy at the end of the season, beating Young Boys in the final after a penalty shoot-out.

Europe Champions League qualifying round As Swiss champions, Basel entered the UEFA Champions League third qualifying round and their aim was to reach the group stage. However, they were drawn against German Bundesliga club Werder Bremen and they lost 4–2 on aggregate. Three goals in eight second-half minutes in the return leg swung the tie decisively in the German side's favour.

Werder Bremen (10 August 2005) Goals in either half from David Degen and substitute Julio Hernán Rossi ensured Christian Gross's side the advantage before the return leg at the Weserstadion on 24 August. However, the German team still had every confidence of overturning the deficit, thanks to Miroslav Klose's strike on 72 minutes. Thomas Schaaf's men were behind after 27 minutes after some lax defending. Goalkeeper Andreas Reinke was stranded after Scott Chipperfield's shot had been blocked and Degen made no mistake when well placed. The wayward defending continued into the second half, allowing Argentinian striker Rossi to double the home team's advantage on 52 minutes by drilling through Reinke's legs to the obvious delight of a sell-out 29,000 crowd at St. Jakob Park. Yet the home fans were given pause for thought when Germany forward Klose pulled one back in the closing stages.

Return match (24 August 2005) Three goals in eight second-half minutes swing the tie decisively in the German side's favour. Until the opening goal Basel had protected Pascal Zuberbühler's goal with some ease, but a fortuitous deflection unhinged their defence after 63 minutes. A clearance from the Basel defence hit Patrick Owomoyela on the chest and the ball bounced into the penalty area, Bremen striker Ivan Klasnić was quickest to react and he tapped the ball into the empty net from close range. Basel found themselves further in arrears moments later when Johan Micoud was fouled in the penalty area by Reto Zanni. Tim Borowski made no mistake, slotting the ball into the bottom left-hand corner. The home side then guaranteed their spot into the draw for the next round, with Klasnić's second goal after 72 minutes. The striker latched on to Daniel Jensen's pass to send a left-footed strike in off the post beyond Zuberbühler from 15 metres.

UEFA Cup Subsequently Basel dropped into the 2005–06 UEFA Cup, where they met Bosnian club NK Široki Brijeg in the first round.

NK Široki Brijeg (15 September 2005, 29 September 2005) In the first leg of the first round Basel played at home in the St. Jakob-Park and Matías Delgado scored a hat-trick as Basel won 5–0. The return match in Široki Brijeg was also won. Basel sealed a 6–0 aggregate win to qualify for the Group stage.

Group stage Here Basel were then drawn into Group E, alongside Strasbourg, Roma, Red Star Belgrade and Tromsø.

RC Strasbourg (20 October 2005) Basel lost their first home match against Strasbourg 0–2 after defender Patrick Müller was sent off for pulling down Amara Diané in the 33rd minute. Diané himself had put the guests one up in the 15th minute and fellow Ivorian Arthur Boka scored a second ten minutes later.

Red Star Belgrade (3 November 2005) An away win against Red Star Belgrade in the second match day. Rossi ran on to a pin-point pass from Matías Delgado with just two minutes remaining as Basel vanquished memories of their 0–2 defeat by RC Strasbourg on Matchday 1. It completed a well-earned turnaround after Milan Purović had given the home side the lead midway through the first half. Basel soon drew level when Delgado converted a penalty on the half-hour mark, paving the way for a thrilling win.

Tromsø IL (1 December 2005) The Basel side rallied from being 1–3 down after 29 minutes to secure an unlikely 4–3 win to move second, while eliminating Tromsø. Tromsø had gone ahead as early as the second minute when Lars Iver Strand headed in Ole Andreas Nilsen's cross. Basel attempted to respond and came close a minute later, only for Eduardo to header over the bar, while 60 seconds later Matías Delgado also shot wide. Petrić did equalise as he fired in a left-footed shot after Smiljanić had headed Patrick Müller's free-kick into his path. However, Tromsø regained their lead three minutes later when Ole Martin Årst collected Joachim Walltin's pass before hitting an angled shot into the net from 12 metres. After 29 minutes the visitors opened up a 3–1 lead and this time Årst was the provider, playing the ball from the right for Strand to score his second of the evening. Basel piled on the pressure in the second half but were almost caught out when Patrice Bernier's header forced a save from Pascal Zuberbühler. Delgado reduced arrears when he converted a cross from Petrić just after the hour and it was all-square six minutes later when Scott Chipperfield headed in a Julio Hernán Rossi cross. With 16 minutes remaining, Basel took the lead for the first time as David Degen collected an Eduardo pass and scored from close range. Basel secured the most unlikely of wins to move into second place in the standings.

AS Roma (14 December 2005) An away defeat against Roma followed. Roma pressed from the very first moment and it was inevitable that Rodrigo Taddei put the home team one up after just 12 minutes. But Basel reacted and fought back. Ivan Ergić saw his header rebound from the cross bar after 25 minutes and Delgado's shot rebounded from the post just two minutes later, but the equaliser did not fall. In fact Francesco Totti put the home team two up just seconds before the half time whistle and shortly after the start of the second period Shabani Nonda added a third goal. With this three goal lead, AS Roma just tried to control the game and played just in midfield. Towards the end of the game Basel turned up their efforts and after 78 minutes Mladen Petrić pulled a goal back. But it wasn't enough to turn the game and Basel lost 1–3. Because, at the same time, Strasbourg scored the 2–2 equaliser in the fourth minute of over time against Red Star Belgrade, with some luck Basel qualified for the knock-out stages.

AS Monaco (15 February 2006)