East Midlands Trains said services were delayed between Luton and Bedford from about 10:30 GMT due to the injured bird near Flitwick station.
A spokesman said the swan was removed just before 11:00 GMT. The RSPCA said it had to be put down.
Trains on the line run between London St Pancras and Bedford and on to Nottingham and Derby. Thameslink services were also affected.
Trains were expected to return to normal before midday.
An RSPCA spokesman said the swan was put to sleep by a vet. It was not known if it was injured by a train.
"The bird's leg had been totally shattered and the vet considered it the most humane thing to do to prevent further suffering," he said.
Trains were halted in Bedfordshire after a swan was seen on the line.