Having joined the company in 2014, Mr Carne will step down from his position later this year.
A new Chief Executive will be stablished before the start of the next five year regulatory control period, which begins in April 2019.
Speaking on his decision, Mr Carne said: "The men and women who run the railway are enormously committed and it has been a privilege to lead the organisation at a time of huge investment and transformational change.
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"I planned the timing of my announcement so there was stability while we developed the business plan for the next five year regulatory period, but so that there will also enough time for my successor to be firmly in place when it starts. I will leave knowing that the railway is in good hands and has a great plan for the future."
Chris Grayling, Secretary of State for Transport said: "Mark has done an excellent job as Chief Executive of Network Rail, presiding over the biggest modernisation of our rail infrastructure since Victorian times.
"Mark will of course continue to provide great leadership for Network Rail until he steps down in the summer, and I hope he will continue to play an important part in the transport sector in the future."
(LM)
