Philadelphia Inquirer said the injuries were minor and the incident took place just before 6 p.m Saturday.
The spokesman, Andrew Busch, said the engineer was taken to the Hospital of the University of Pennsylvania.
Philadelphia police said they are looking for the person who threw the rock.
Busch said these incidents are rare.
"We do have instances of vandalism and things like that. But something like this,in terms of rocks being thrown at trains, especially one that's in service -- it does not occur too frequently," he said.