The not-for-dividend company, which has no shareholders, said former Shell executive Mark Carne, 54, will succeed Sir David Higgins on April 1 next year.
NR said father-of-three Mr Carne would be on a basic annual salary of £675,000. This compares with Sir David's figure of £591,000.
NR has faced constant criticism recently over train punctuality, with repeated warnings by rail regulators about its performance, particularly on long-distance routes.
NR said today: "Mr Carne's base salary of £675,000 was determined following an exhaustive and independent process which compared the salaries of chief executives in both the public and private sectors given Network Rail's unique position as a not-for-dividend, independent company.
"The review concluded that the proposed salary reflected that unique status placing, as it does, the chief executive's salary at a point between the two sectors."
It added: " Mr Carne will not take any potential annual incentive payment for 2013/14."
NR chairman Richard Parry Jones said: "Through his work with Shell and BG Group in very testing and difficult environments, Mark Carne has shown that he has the necessary skill and global experience to build on, and develop further, what Network Rail has already achieved in meeting these challenges under the leadership of David Higgins. We thank David for all he has done for the company."
Mr Carne said: "The success of Network Rail is vital for Britain's economy and this is an exciting time for the whole rail industry. I am delighted to be given the opportunity to lead Network Rail and look forward to working with the team to drive performance to new heights."
Manuel Cortes, leader of the TSSA transport union, said the level of Mr Carne's salary was "an insult to rail passengers who have seen price rises of 20% since May 2010".
Mr Cortes added that Mr Carne stood to earn large bonuses over the next three years.
Bob Crow, leader of the RMT transport union, said: " Clearly this sizeable pay increase sets a benchmark for the rest of the rail industry and in the interests of fairness RMT will be factoring it in to our pay negotiations on behalf of the many thousands of NR staff."