Over the many years of operation there have been a number of serious accidents. Amongst the most recent, on 3 August 2003 a car and train were in collision at an ungated level crossing, protected by flashing warning lights. The train driver, 31-year-old Kevin Crouch, died; some passengers were treated for shock and minor injuries; locomotive number 5 (Hercules) was seriously damaged. The female car driver, whose baby was a passenger in the vehicle, had ignored or failed to see the warning lights. The woman and her baby were taken to hospital, but were not badly hurt. The railway and the Health and Safety Executive instigated an investigation, and the woman was arrested on suspicion of causing death by dangerous driving. Although acquitted, she was found guilty of the lesser charge of careless driving. On 10 July 2005 a car and train were in collision at another level crossing under similar circumstances. The driver of the train, Suzanne Martin, wife of the railway's general manager, Danny Martin, was killed; several passengers were treated for shock; locomotive number 8 (Hurricane) was seriously damaged. The car driver, a 20-year-old man, had ignored or failed to see warning lights; he was arrested at the scene, and later bailed by Kent Police.
Following the two incidents detailed above, the railway has begun a programme of level crossing refurbishment. There are a number of 'occupation crossings' where the railway meets farm tracks, with local control; but of the eighteen junctions of the railway with public highways, five are road bridges, and the other thirteen are level crossings. All level crossings have been protected since the 1970s by flashing warning lights (AOCL); the refurbishment programme will see the additional installation of lifting half-barriers, upgrading the crossing to ABCL status, each refurbishment costing around £90,000. Those already altered in this manner are Burmarsh Road (site of the 2003 accident), Battery Road (site of the 2005 accident), Botolph's Bridge Road, and St Mary's Road in Dymchurch. The next level crossing to be upgraded will be Jefferstone Lane, adjacent to St Marys Bay station