Work on the 86-acre (35-hectare) site, which is behind the city's railway station and owned by the rail firm, is due to start next year.
Senior councillors in York agreed last December to spend Â£10m to improve access including creating a bridge.
Both organisations have signed a Memorandum of Understanding (MoU).
Network Rail said it was "a very positive step towards developing this challenging site".
Phil Verster, managing director for Network Rail, said: "We have been working hard with City of York Council to produce a plan which will allow phased and achievable development, and which uses this large piece of land to maximum benefit for York residents and businesses alike."
Council leader James Alexander said the development was "crucial to grow the city's economy".
A public consultation on the plans for the site is due to start over the coming months.
An agreement to start the development of 480 homes, shops and offices in York has been sealed by Network Rail and council leaders.