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Officials said human passengers were evacuated to other cars and a Network Rail employee tried to use food to lure the animals off the train at a stop in Redhill.
The train was ultimately sent back to Reading when one of the squirrels refused to leave.
"We can confirm that the 0854 Reading to Gatwick was terminated at Redhill after a couple of squirrels boarded the train at Gomshall without tickets, breaching railway byeclaws," a GWR representative told the BBC. "We attempted to remove them at Redhill, but one refused to leave and was returned to Reading to bring an end to this nutty tail."