The Virgin Train was halted at Peterborough at about 15:00 GMT on New Year's Day after the arachnid made an unexpected appearance, police said.
It was scooped up in an ice cream tub and taken to a nearby pet refuge.
"Happy to confirm we quickly took the sting out of the situation," British Transport Police tweeted afterwards.
Staff at The Exotic Pet Refuge in Deeping St James said it might be tricky to identify the species of their new guest.
"I was told the woman whose bag it came out of had recently come back from Guatemala - and there are 100 different kinds of scorpion there," said refuge centre owner Pam Mansfield.
"It's only small - about three quarters of an inch - and it's jet black with very fine little pincers.
"Usually, the smaller they are, the deadlier they are - so it could be quite a nasty piece of work. But we'll treat it with care."
A train service from London to Edinburgh had to be stopped by police after a scorpion crawled out of a passenger's bag.