On 30 January 2011, Schalke 04 formalized his arrival. Charisteas signed a contract on 30 June 2011, until the end of the season. In his debut match for Schalke, he scored the second goal in a 2–1 home win against Eintracht Frankfurt. It was his first touch of the ball, having been on the pitch for only 52 seconds. On 13 April 2011, Charisteas reached the semi-finals of the 2010–11 UEFA Champions League with Schalke, beating in the quarter-finals the defending champion Internazionale, Charisteas replaced the Brazilian Edu in the 32nd minute of the second half. Schalke 04 and Charisteas reached a result never achieved before.
On 21 May 2011, Charisteas won the German Cup with Schalke 04.
On 27 July 2011, Charisteas joined Panetolikos, newly promoted to the Super League, signing a one-year contract. His first goal of the season came on 14 September 2011 when he scored the winning goal in the 1–0 home win against Asteras Tripolis.
Charisteas was called up again on 8 October 2011 for the qualification match against Croatia, and on 11 October 2011, where he scored the winning goal in the 85th minute in Georgia, securing a 2–1 victory which sent Greece automatically to the Euro 2012 Championships. With this goal, Charisteas score in three qualifiers for European Championships and for three consecutive World Cups, became the only player to reach that in the Greek national team.