Gundogan has not featured for Dortmund since the 0-0 draw against Bayern Munich in the Bundesliga on March 5 due to a foot problem.
But the 25-year-old Germany midfielder took part in a training session with Thomas Tuchel's team two days ahead of Jurgen Klopp's highly anticipated return to Signal Iduna Park with Liverpool.
Gundogan has been heavily linked to a move away from Dortmund at the end of this season, with incoming Manchester City boss Pep Guardiola reported to be keen on securing his signature.
Addressing the speculation last month, Tuchel said: "Am I convinced that he will stay put? I will only be convinced he will stay once he signs a new deal.
"Ilkay knows what Dortmund are all about. He knows that he can develop here and become one of the team's leaders. He knows what he has at Dortmund."
Captain Mats Hummels and fellow defender Sokratis Papastathopoulos also resumed training with Tuchel's squad on Tuesday after sitting out Saturday's 3-2 win over Werder Bremen.