Officers from British Transport Police were called to the scene of the incident on the outskirts of Aberdeen but could find no trace of the man.
But he later walked in to a local police station and was taken to hospital to have his injuries assessed.
Last week rail services on the line were disrupted for three days in succession following a series of cable thefts and vandalism incidents on the track caused by metal thieves.
Last night’s train between Inverness and Aberdeen was held up at Dyce for almost an hour while investigations were carried out.
A British Transport Police spokesperson said: “BTP officers were called to the line near Old Meldrum Road, Aberdeen, on Tuesday, following a report that a man had been struck by a train.
“Officers attended the incident, which was reported to BTP at 8.05pm, and carried out an extensive search of the area, but to no avail.”
He continued: “The man presented himself at a local police station later that evening and has been taken to hospital for an assessment. His injuries are not thought to be serious.”
The 6.13pm Inverness to Aberdeen service, due to arrive at 8.32pm, was delayed for almost an an hour. The line reopened at 9.15pm.