Network Rail, the company that replaced Railtrack, has made an annual pre-tax loss of £232m, up from £47m last year.
Hundreds of miles of new track have been laid in the past year
The increased loss is mainly down to paying interest on money it has borrowed to fix the railway network.
The "not-for-dividend" firm says train punctuality is at a six-year high, and £3bn has been invested in the network, including 700 miles of new track.
The firm, whose top executives are due to receive big bonuses, hopes to be in the black this financial year.
"Punctuality is getting back to what it was before the Hatfield rail disaster in 2000," Network Rail chairman Ian McAllister told the BBC.
"But we have still got a lot to do to get to an operating level satisfactory to all our customers."
Mr McAllister also defended bonuses for chief executive John Armitt, who is on a basic salary of £504,000, and pointed out that all members of staff will receive a bonus.
Deputy chief executive Iain Coucher, finance director Ron Henderson and projects and engineering director Peter Henderson are also expected to receive sizeable pay-outs.