The man climbed the tree near Charlton station, south-east London, at about 02:00 BST after being tracked by officers and a police helicopter.
British Transport Police (BTP) said he climbed down the tree near Barney Close, at about 19:00.
The 32-year-old was arrested on suspicion of burglary and the obstruction of trains with intent.
Rail operator Southeastern said it had to suspend services while the man refused to come down as it was too dangerous to continue running trains in the area.
Earlier in the day a statement on its website said: "Because of an ongoing trespass incident, our services via Woolwich Arsenal and Greenwich may be cancelled, delayed or diverted via Bexleyheath."
About 20 BTP officers attended the scene and scaffolding was put up next to the tree to get close to the man.
Cherry pickers were also used and negotiators spoke to the man in an attempt to coax him down.
A man suspected of burglary who climbed a tree to evade police has caused disruption to commuters in London.