Great Western Railway (GWR) services were suspended between Guildford and Reading shortly after 06:15 BST.
The man suffered life-threatening and life-changing injuries when he was struck near Wellington College, South Central Ambulance said.
GWR said passengers faced delays of up to an hour before services resumed with some residual disruption.
Rail passengers faced delays when a man was hit by a train at Crowthorne, near Reading.