The actor, 58, is in the area to shoot scenes for his upcoming project Mission: Impossible 7, which is scheduled for release in May 2022.
Location shoots have already taken place in Venice, Rome, Surrey and Norway, and it is thought the current travel restrictions may have forced changes to the schedule.
The crew hired Levisham Station on the North Yorkshire Moors Railway, which is currently closed to the public, and the sidings were used for the filming.
Two freight locomotives could be seen alongside several crew members.
Cruise was also seen in Pickering yesterday and a helicopter associated with the shoot flew over Scarborough, and he was photographed on the set by dog walkers and a local B&B owner.
The star was recognisable despite wearing a nondescript black outfit and a face covering.