Those travelling on the Penistone to Huddersfield Northern service, which cuts across Barnsley and Denby Dale, are facing delays of an unspecified time.
Trains have been replaced with rail replacement bus services, but passengers have been warned that the 'rural nature' of the route will mean significantly longer journey times.
A tweet from Northern said: Due to a train hitting an object, the line between Huddersfield and Penistone is blocked in both directions. Staff are en route to assess the damage and put together a plan going forward but as yet there is no estimate for the resumption of the service.
"Road replacement transport has been requested to operate between Barnsley and Huddersfield.
"Please be aware that due to the rural nature of the route journey times will be significantly increased when using road replacement."
Delays are expected until at least 4pm.