Stocker began his career at SC Kriens, for its youth teams he played from 1996 to December 2005. From January 2006 he played for the Under-21 team of FC Basel. In summer 2007, he was promoted to the first team of FC Basel, with the Swiss champion and he 08 Swiss Cup winner was in season 2007 /. In the 2008 /09 season he played with FC Basel in the UEFA Champions League and was voted the best young player of the Swiss league. In the seasons 2009/10 and 2010/11 Valentin Stocker was again Swiss champion with FC Basel.
Stocker retired April 23, 2011 in the match against BSC Young Boys cruciate ligament injury. It was his hundredth Super League match. he was operated on two days later. His first game after the injury break was 3 December 2011 in a 1-0 home win against FC Luzern. On the same day it was announced that Stocker extended his contract ahead of schedule for two additional years until the end of June 2016.
At the end of the 2012/13 season Stocker was with FC Basel for the 5th time Swiss champion and the team was in the Cup final, which they lost in a penalty shoot only. In the UEFA Europa League 2012/13 he managed with FC Basel to the semi-finals where he performed against the reigning UEFA Champions League winners FC to Chelsea. However, they lost the Home and Away match and eliminated in the total score of 2-5 from. In a long season with a total of 76 games ( 36 in Super League, 6 in Cup, 20 in the Champions League and Europa League, including 14 test matches ), he had a total of 62 operations, including 31 in the Super League, 3 in the Cup, and 17 inserts in the Champions and Europa League and 11 in test matches.
Stocker graduated seven games for the Swiss U21 national team. On August 20, 2008 Stocker made his debut in the Swiss national football team. In the game against Cyprus, he was in the starting lineup and scored his first goal equal.
- Swiss champion with the U18 FC Basel: 2006
- Swiss Cup winner with the U18 FC Basel: 2006
- Swiss champion (5): 2007/ 08, 2009/10, 2010/11, 2011/12 and 2012/13
- Swiss Cup winner: 2007/ 08, 2009/10, 2011/12
- Swiss Cupfinalist: 2012/13
- Uhrencupsieger: 2008, 2011, 2013