Clapton railway station is on the Suburban Line operated by WAGN Railway, of North London railway. It links Upper Clapton to Liverpool Street in central London, and to Hertford East and Enfield Town further north. Trains generally run every fifteen minutes.

Clapton is on the branch of the Lee Valley lines that separates into Tottenham Hale or St James Street. It joins up with the Seven Sisters branch at Hackney Downs.

Clapton is in both Travelcard Fare Zone 2 and Travelcard Fare Zone 3.