A fallen tree caused train cancellations between Fareham and Southampton St Denys this morning.
Services were halted because the tree, which toppled as strong winds lashed the area, was blocking the line at Netley.
All lines re-opened at about 7.10am today, but passengers are being advised to expect delays.
A spokesman for Network Rail said the Southern train hit a small silver birch tree at about 6am today.
The train was travelling from Barnham, West Sussex, to Southampton.
The spokesman told The News: ‘A small silver birch fell on the line. The driver obviously saw the tree and put the brakes on.
‘The birch tree was lodged under the front wheels of the train.
‘No-one was hurt.’
He said the train would probably have been travelling at about 60mph when the impact happened.
The train was stuck for 45 minutes before engineers came and removed the tree.
Meanwhile, people are being advised to brace themselves for windy weather as gales are set to batter the south coast later today.
Gusts of up to 40mph could affect the Portsmouth area this afternoon.
The winds will continue into the night, but should ease by tomorrow.
It comes as a low pressure system moves across the country, with the south west and Wales bearing the brunt of the weather, with gusts of up to 70mph and extremely heavy rain.
Pete Fox, the Environment Agency’s head of flood risk strategy, said: ‘There is already significant travel disruption due to the wet weather and we would urge people to remain vigilant as further flooding is possible across the South West.’
Sally Webb, forecaster with MeteoGroup, said: ‘This weather is very common for autumn, it is just unfortunate that it seems to keep coming at the moment.’
Condor Ferries is running a revised service for the Commodore Clipper because of the bad weather.
The service from Portsmouth to Guernsey will depart the ferry port at 9am and the estimated arrival time has been changed from 8.30pm to 4pm.
The ferry from Guernsey to Portsmouth will depart at 5.20pm, instead of 10pm, and is set to arrive at about 6.30am tomorrow.
The service from Jersey to Portsmouth will depart at 10.05pm, instead of 6.35pm, and will arrive at 6.30am tomorrow.