Profit before tax rose 39% to £1.04 billion for the 12 months ending in March while 90% of passenger trains ran on time, compared to 90.9% the year before.
It means NR again failed to meet a target of 92.5% as it admitted train performance was disappointing.
The company said this was partly down to "slower improvements in asset reliability" though some of the shortfall was also caused by congestion as passenger numbers grew, as well as extreme weather.
Meanwhile, NR's debt pile, which is guaranteed by taxpayers, increased by 9% to £33 billion. It said the profit hike was largely the result of accounting gains on financial hedging instruments.
Meanwhile, passenger numbers grew by 5.7% to 1.6 billion during the year.
NR said this meant numbers had doubled since 1995.
Chief executive Mark Carne said: "We are in the middle of a rail renaissance, with record levels of passenger numbers and record levels of investment. This flourishing sector is investing heavily to improve the railway for today and for tomorrow."
Mr Carne said with more trains on the network than ten years ago, there were "inevitable challenges".
"We are determined to do more to improve train reliability in the face of these challenges," he added.
Finance director Patrick Butcher said: "We have been disappointed with train performance but celebrate continued strong growth, savings made, swiftly repairing the railway following extreme weather."