There was major disruption on the train line after the incident, which was first reported just before 8pm.
Emergency services assisted at the scene, to help passengers off the stuck train.
"It is with great sadness that we report a person has been hit by a train between Chichester and Barnham," a spokesperson for Southern Rail said.
"All lines are blocked between these stations whilst the emergency services work to deal with this incident."
For nearly three hours, trains were unable to move between Barnham and Chichester. This caused significant disruption to Southern services to /and from Portsmouth and Southampton Central.
Rail replacement buses were in operation and passengers were warned that journey times could take up to 60 minutes longer than usual.
In an update just before 10pm, a Southern spokesperson said: "British Transport Police are currently working with our Network Rail colleagues to help our passengers safely off the stuck train and away from the track."
Lines were reopened an hour later, with disruption cleared by 12.30am.
The spokesperson for the train company added: "We work closely with Samaritans and support the work they do.
"If you or someone close to you has been affected by this or any incident, there is always someone to talk to. Contact Samaritans on 116 123 free at any time, on any phone. Help and advice is only a phone call away.
"If your journey has been delayed by 15 mins or more, you can claim Delay Repay compensation which you can choose to donate to Samaritans to support their life-saving work."