Toprak began his career with TSB Ravensburg in 1994. In 2001, he moved to FV Ravensburg.

Toprak signed for SC Freiburg in 2005. Three years later, He signed his first professional contract in the 2007–08 season. During that period, he played for Freiburg U19 and the reserve team and won 22 games with the latter.

In his first professional season, he featured in 26 league games and scored 4 goals as Freiburg won the 2. Bundesliga and promoted after a defeat of VfL Osnabrück. On 9 June 2009, Toprak suffered from a karting accident, causing him to miss the first half of the 2009–10 season but he recovered, scoring a goal against Hamburger SV on the 65th minute. Toprak played 24 league games during the 2010–11 season.

On 9 June 2009, Toprak was involved in a karting accident, in which he suffered severe burns and had to be treated in a special clinic. He was able to resume training after only four months.

On 30 September 2011, Toprak was named to the Turkey national football team squad by coach Guus Hiddink for the upcoming UEFA Euro 2012 qualifying matches against Germany and Azerbaijan. He made his Turkish debut on 15 November against Croatia in the second leg of UEFA Euro 2012 qualifying play-offs, playing the full 90 minutes of a goalless draw at the Stadion Maksimir in Zagreb which ensured that Croatia advanced to the finals 3–0 on aggregate.

In January 2014, Toprak agreed a contract extension until 2018.

In August 2019, Toprak joined Werder Bremen on a year-long loan from Borussia Dortmund. Werder Bremen announced the deal includes an purchase obligation to permanently sign Toprak that would come into effect with a “high likelihood”; the reported transfer fee agreed for that case was reported as €5 to 6 million. The permanent signing took effect in July 2020.