In committing to the Office of Rail Regulation (ORR) plans, NR will also aim to bring down the costs of running the railways by 20% for the five-year period starting in April 2014.
NR will have to meet a target of running 90% of trains on time on London, south east England, regional and Scottish services and improving reliability on long-distance trains.
The company is also signing up to improved standards of infrastructure management, network resilience, and safety for passengers and railway workers.
Over the next five years, NR will spend more than £38 billion on maintaining, renewing and improving the rail network.
ORR chief executive Richard Price said: "Service standards will get better, as stations up and down the country are modernised and lines are electrified. Alongside this work, the company will also deliver more, pound-for-pound, than ever before, as it utilises new technology and better ways of working."
He added: "This is a fresh start for the company and an opportunity, supported by significant levels of funding by governments and passengers, and working with the rest of the industry, to learn lessons and build on successes from the past.
"Meeting these challenges will be tough. We will focus on ensuring the company, working with governments and the rest of the sector, delivers its plans to achieve long-term and sustainable improvements for customers and taxpayers."