Banbury train station in Oxfordshire has reopened after it was closed when a man scaled the signal gantry.
British Transport Police said the man, who is in his 20s, is now down from the gantry. He has been taken to hospital with serious injuries.
The incident started just before 10:00 BST with some passengers reporting being stuck on trains for five hours.
Officers have said they were aware of reports the man had a knife and trained negotiators had been talking to him.
Tom Hayes, was travelling from Birmingham to London. He was stuck on a stationary train for five and a half hours.
He said: "We managed to keep up to date on Twitter and Facebook. We got a couple of updates from the driver, who walked through the train, but we didn't really know what was going on."
Having missed the filming he was travelling to London for, Mr Hayes decided to return to Birmingham.
He said: "We've just arrived at Banbury station but I've given up now and I'm going home. Trains are running now, albeit in an ad-hoc way."
A British Transport Police spokesman said trains had been stopped while the incident was ongoing.
He added that officers had voluntarily referred the matter to the Independent Police Complaints Commission.
Jennifer Payne, customer service director at Chiltern Railways, said services were "heavily impacted" by the incident and apologised to customers.
She said: "The line has now reopened but passengers may experience delays and short notice cancellations whilst we try and get services back to normal and trains back to their usual positions.
"Customers impacted by the disruption may be eligible for compensation and those affected should complete a form either at one of our stations or by visiting our website."