The train made an emergency stop after the reptile was spotted lurking on a baggage rack in a carriage headed to Jakarta from Bogor, south of the capital.
Smartphone footage, which quickly went viral, showed the bespectacled man casually snatch the snake's tail and then smash its head on the floor in a violent whipping motion.
Warning, footage may be distressing.
The creature was apparently killed instantly as shocked spectators, including a baton-wielding transit security officer, kept their distance.
The unidentified man wearing a backpack then tossed the snake, which appeared to be about one metre (three feet) long, out the door to waiting security staff.
It is not clear what kind of serpent it was, nor whether it was venomous. No injuries to passengers were reported.
The man has been both praised and criticised on social media for his actions.
Many felt the action was cruel, however, others argued if the snake were venomous it may have put passengers lives at risk.
Train operator KCI said the reptile is thought to have slithered out from a passenger's bag.
The spokesman suspected the snake was intentionally carried on the train.
"We regret the incident and apologise to train travellers who were disturbed by it," spokeswoman Eva Chairunnisa told AFP.
It is not uncommon to see livestock or pets travelling on public transport in rural Indonesia, but passengers are prohibited from taking animals on urban transport lines.
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