Hyypiä became part of the coaching staff for both Finnish national team and Bayer Leverkusen.
He started a coaching formation at the Football Association of Finland.
In October 2011, Hyypiä was in Leverkusen for six weeks as a trainee with the club's then-head coach, Robin Dutt.
On 1 April 2012, Hyypiä and under-19 coach Sascha Lewandowski were named as caretaker coaches of Leverkusen after the sacking of Dutt.
On 15 May 2012, Hyypiä was confirmed as team manager and Lewandowski as head coach of Bayer Leverkusen until the summer of 2015.
In an unusual managerial set-up, both are equally responsible for leading Bayer Leverkusen: as Lewandowski has the training licence, he had to be at post-match press conferences and took care of the training sessions.
Meanwhile, Hyypiä watched them, intervened with personal talks and was at the pre-game press conferences.
Despite his imperfect grasp of the German language, Hyypiä addressed the team before matches.
This system proved successful: in the middle of the 2012–13 season, Leverkusen was second in the Bundesliga, were the only side to beat Bayern Munich at home and qualified for the next round in the Champions League, and the DFB-Pokal.
Bayer Leverkusen ended the 2012–13 season in third place behind the champions Bayern and runners-up Borussia Dortmund.
Hyypiä became the sole head coach after Lewandowski went back to work with the youth development department.

Hyypiä's first training session as the sole head coach occurred on 24 June 2013.
Bayer Leverkusen ended the 2013–14 season in fourth place, behind Bayern Munich, Borussia Dortmund and Schalke 04.
On 5 April 2014, Hyypiä was sacked by Bayer Leverkusen with immediate effect after the club lost to Hamburger SV the night before.
Hyypiä became part of the coaching staff for both Finnish national team and Bayer Leverkusen. He started a coaching formation at the Football Association of Finland. In October 2011, Hyypiä was in Leverkusen for six weeks as a trainee with the club's then-head coach, Robin Dutt. On 1 April 2012, Hyypiä and under-19 coach Sascha Lewandowski were named as caretaker coaches of Leverkusen after the sacking of Dutt. On 15 May 2012, Hyypiä was confirmed as team manager and Lewandowski as head coach of Bayer Leverkusen until the summer of 2015. In an unusual managerial set-up, both are equally responsible for leading Bayer Leverkusen: as Lewandowski has the training licence, he had to be at post-match press conferences and took care of the training sessions. Meanwhile, Hyypiä watched them, intervened with personal talks and was at the pre-game press conferences. Despite his imperfect grasp of the German language, Hyypiä addressed the team before matches. This system proved successful: in the middle of the 2012–13 season, Leverkusen was second in the Bundesliga, were the only side to beat Bayern Munich at home and qualified for the next round in the Champions League, and the DFB-Pokal. Bayer Leverkusen ended the 2012–13 season in third place behind the champions Bayern and runners-up Borussia Dortmund. Hyypiä became the sole head coach after Lewandowski went back to work with the youth development department.
Hyypiä's first training session as the sole head coach occurred on 24 June 2013. Bayer Leverkusen ended the 2013–14 season in fourth place, behind Bayern Munich, Borussia Dortmund and Schalke 04. On 5 April 2014, Hyypiä was sacked by Bayer Leverkusen with immediate effect after the club lost to Hamburger SV the night before.
Sami Hyypiä