The commission said in a statement that it undertook "unannounced inspections" at the premises of Deutsche Bahn and some of its subsidiaries.
"The commission has reason to believe that Deutsche Bahn may have breached EU anti-trust rules that prohibit the abuse of a dominant market position," the statement said.
It said the surprise inspections were "a preliminary step" investigating "suspected anti-competitive practices" but insisted this "does not mean that the companies are guilty of anti-competitive behaviour nor does it prejudge the outcome of the investigation itself."
Deutsche Bahn said offices in Berlin, Frankfurt and Mainz had been visited by the commission's inspectors.
The searches stemmed from allegations that Deutsche Bahn Energie, de facto sole electricity supplier for traction trains in Germany, offered preferential treatment to the group's rail freight arm.
The commission said its officials were accompanied by counterparts from the German competition authority during the inspections.
The head of the railway's judicial services unit, Gerd Becht, told a press conference in Berlin that Deutsche Bahn was "surprised by the searches.”
"This pricing system has been in place since 2002," he added. "We consulted the German anti-cartel office at the time and won several cases." He did not provide further details.