Having started his training with FC Alemannia München, Lell earned a place in Bayern's youth section in 1993, and played there for eight years.
For the 2001–02 season, Lell was a part of Bayern's reserve team. In his first season at the senior level, the right-wingback made 10 appearances in the Regionalliga Süd. He would make 31 league appearances and a cup appearance during the 2002–03 season. He made 20 appearances for the reserve team during the 2003–04 season. Lell made his Bundesliga debut on 4 October 2003 in a 4–1 against Hertha BSC where he came on as a substitute for Michael Ballack in 84th minute. He made three subsequent appearances for Bayern in Bundesliga play and a cup appearance during the 2003–04 season.
To the beginning of the 2004–05 season, Lell was loaned to 2. Bundesliga club 1. FC Köln, where he had a disappointing season. After the 4–2 loss to Wacker Burghausen on the second matchday, Lell fell out of favour with manager Huub Stevens. He earned a mere sixteen league appearances over the course of the season. The season however wasn't entirely without successes for Lell. In Köln's second league match against Wacker Burghausen he scored a goal. Beyond that, he earned two caps in the DFB-Pokal, and eight for the reserves in the Regionalliga Nord. After the "Billy goats'" successful return to the Bundesliga for the 2005–06 season, Lell earned considerably more appearances, especially during the latter half of the season, during which he advanced to the regular starting formation. He finished the season with 26 league appearances and a cup appearance.
For the 2006–07 season, Lell returned to Bayern, appearing 16 times for the first team and eight times for the reserve team. The 2007–08 Bundesliga season meant a lot to Lell. Because of the injury problem to vice-captain and starting right-back Willy Sagnol, Ottmar Hitzfeld decided to put Lell into the starting line-up as the right fullback. In this season, Lell earned 29 appearances in the Bundesliga, scored his first Bundesliga goal. In the German Cup, he played eight matches, in the UEFA Cup, he played 11 matches and scored one goal, and three times in the league cup. During the 2008–09 season, under coach Jürgen Klinsmann and interim coach Jupp Heynckes, Lell made 28 appearances in all competitions.
On 1 September 2009, just before the transfer window closed, Bayern and Premier League club Stoke City came to an agreement for Lell transfer to England. However, the deal failed when no one was able to contact Lell and inform him about it. As a result, the transfer window closed before Lell could agree to the transfer. In the 2009–10 season, new Bayern coach Louis van Gaal relegated Lell to the reserves, where he made an appearance. He almo made an appearance in the cup for the first team.
Seven years after making his debut with first team, he left the Bavarian side and signed for Hertha BSC on 23 June 2010. This ended a 17-year connection dating back to 1 July 1993 when he joined Bayern Munich's youth academy. His contract in Berlin ran for one year, and was automatically extended for an additional two as Hertha earned promotion to the Bundesliga. Lell has quickly established himself as an important part of Hertha's defense, having started almost every fixture so far and assuming vice-captaincy of the team. He finished the 2010–11 season with 33 league appearances and two cup appearances. He would go on to 28 league appearances, two cup appearances, and an appearance in the relegation playoff.
On 7 June 2012 Lell was released along with Patrick Ebert, Andreas Ottl, and Andre Mijatovic. The decision to part company with Lell came a day after he was given a 5-match ban for insulting referee Wolfgang Stark during a relegation play-off match against Fortuna Dusseldorf. Following his release his agent announced his client was already in discussions with Fulham and West Ham of the Premier League, with Stoke City FC also showing an interest, a club Lell almost signed for in 2009.
Lell signed for Levante on 11 August 2012. The contract is for a season plus a one-year option. He would go on to score two goals in 28 appearances in 2012–13 season and no goals in five appearances in the 2013–14 season.
Lell joined TSV Weyarn on 2 September 2015, who play in the Kreisklasse Zugspitze East. He joined Weyarn for family reasons. Weyarn won three and drew one before Lell joined the club.
Christian Lell represented Germany on the Under-20 team at the 2003 FIFA World Youth Championship.
Lell also holds Austrian citizenship. After voicing desire to play for the Austria national football team, he was found not eligible.
Lell's sister died in April 2014 at the age of 27 from cystic fibrosis. He started a foundation for cystic fibrosis in 2009. Lell is married.
Lell was arrested on 3 January 2014 after his wife filed a report with the police. Lell stated, "I controlled myself. Cause I know how fast you can get into the mill false accusations."As of 19 November 2015.
1.^ Includes DFB-Ligapokal and relegation playoff.
Bundesliga: 2007–08, 2009–10
DFB-Pokal: 2007–08, 2009–10
DFB Liga-Pokal: 2007
1. FC Köln
2. Bundesliga: 2004–05