The plan is to build a minimum of 480 new homes and up to 80,000m2 of office space, with site preparation starting in 2015 and construction work following in early 2016.
This agreement follows a £10m commitment form the council to kick-start development on the York Central Site.
So far, £27m has been raised for transport infrastructure in and around the site and Station Gateway from the West Yorkshire Plus Transport Fund, and £1.65m for site remediation from the Leeds City Region Local Growth Fund.
Council chief executive Kersten England said: “This agreement is a major milestone in a relationship that we have been developing with Network Rail over the past three and a half years. It signals a significant turning point in both the site’s history, as well as the city’s. It builds on the momentum for brownfield site development seen in Hungate and on the Terry’s site both already in development.
“The site will offer the city an opportunity to address the acute, growing shortage of high-quality office space, as well as addressing the severe challenges the city faces in providing homes for York residents.”