East Midlands Railway (EMR) said a train was damaged in the first recorded incident on 3 February when a large scooter was hurled off a pedestrian bridge near Loughborough station in Leicestershire.
Danielle Clarke, EMR community safeguarding and security manager, said: "These acts are not pranks or a bit of harmless fun, but incredibly dangerous crimes that put customers and staff at serious risk of injury or worse.
Dan Matthews, head of operations delivery at Network Rail, said: "These acts of vandalism not only put lives at serious risk but also cause significant disruption to our rail network.
Builders' waste and masonry were dropped onto a track from the bridge - which connects Allsopp's Lane with Little Moor Lane - and a rock was thrown at a train on 16 February.
She said action was being taken to address the issue, and appealed to members of the public to report any similar incidents or suspicious behaviour on or around railways to British Transport Police.
