The pub was closed for half an hour following the complaint from diner Reece Combs according to the Bath Chronicle.
Company spokesperson Eddie Gershon said: "We can confirm that two rats were spotted in the pub last night. We are aware that one of the rats took a chip that had fallen on the floor from a customer's meal, but can't confirm the fact that it ran up a customer's trouser leg.
"Following the sighting, the pub was closed for 30 minutes and once checks had been made, reopened. Customers in the pub at the time were understanding of the situation. We have since called in pest control experts who have dealt with the situation.
"We are not sure how the rats came into the pub, however, there has been some fly-tipping in the alley at the rear of the pub and this might have been a factor.
"We aim to uphold the highest standards in our pubs at all times and apologise to customers for this situation. We believe it is now under control."
The pub giant was recently found to have one of the best food hygiene rates by the Food Standards Agency, scoring one of the highest proportions of five-star ratings.
In 2014, 91% of JDW pubs scored the maximum five-star rating.