Massachusetts Lt. Gov. Timothy P. Murray announced Wednesday that the State has finalized an agreement to relocate railroad company CSX Transportation’s operations out of Allston—a move that helps pave the way for Harvard to consider long-term development of the many acres of land that the University owns in the area.

Harvard has held land occupied by CSX since 2000, when it purchased 47 acres of land adjacent to the Charles River and in between Harvard and Boston University from the Mass. Turnpike Authority. Three years later, it acquired another 91 acres directly south of that parcel.

But those land holdings—blanketed with tangles of railroad tracks and sliced by the Mass. Turnpike—cannot currently be used by the University because of CSX’s long-standing easements, which restrict the land’s use to railroad operations.

And even this week’s announcement does not give Harvard the ability to develop, as its contracts stipulate that the State maintains the easements if CSX relocates. Harvard will still have to petition the State for development rights.

Because of these hurdles, Harvard refrained from including the 91-acre-parcel—referred to as Allston Landing South—in its 2007 draft Institutional Master Plan, which outlines the University’s development goals for the next 50 years. Portions of the smaller 47-acre-parcel—known as Allston Landing North—were slated for development during later phases of the timeline.

Harvard spokeswoman Lauren Marshall emphasized that the state’s latest announcement “changes very little regarding the state of Harvard’s property at the moment” and that it would be “premature” to begin planning in Allston Landing South, where CSX operates its Beacon Park railyard. But she noted that discussions with the State and CSX “provide optimism that...opportunities for regional economic benefit from this property are closer to a reality.”

Marshall also said that discussions between Harvard, the State, and CSX over the past few years have yielded a “roadmap” outlining conditions that would have to be met before CSX can fully remove its operations from the area and transfer its land holdings to Harvard, including environmental testing and “other important due diligence benchmarks.”

CSX’s Beacon Park railyard has long served as one of the primary and largest entry points for freight shipping to New England. Under Wednesday’s agreement, which reportedly is to be implemented over the next few years, the State will pay $100 million to CSX to take over various railroad tracks and railyards, including those in Allston. The acquisitions are expected to improve and expand commuter rail service in and around Boston.

Jessica Shumaker, a spokeswoman for the Boston Redevelopment Authority, which oversees planning and development in Boston, said that the agreement may help the City develop its proposed rapid-transit Urban Ring around Boston and provide rail service to Allston-Brighton residents.

Paul Berkeley, president of the Allston Civic Association, said it was important to relocate CSX’s operations carefully because switching to less-strategic shipping routes could raise the cost of goods throughout the region. But he praised the agreement and said it would be nice to get the “dirty old railroad out of our neighborhood.”

“That much land, that close to the City—it always seemed like there was a higher use for it,” Berkeley said.

—Staff writer Michelle L. Quach can be reached at mquach@fas.harvard.edu.

—Staff writer Peter F, Zhu can be reached at pzhu@fas.harvard.edu.