Innovation Station in the center of the Dulles Toll Road takes shape during phase II of the Silver Line to Dulles in Herndon, Va. (Katherine Frey/The Washington Post)

Two years after announcing it would take 13 months longer than planned to complete the second phase of the Silver Line, project officials are now putting a price tag on that delay: $95 million.

The money will come out of the project’s $551.5 million contingency fund, so it is not expected to add to the overall cost, said Charles Stark, executive director of the Silver Line rail project.

But the settlement with the contractor, Capital Rail Constructors, may not be the only cost increase associated with the project. There have been 181 change orders associated with building the rail line.

Even so, Stark said he did not anticipate costs to exceed the current $2.7 billion budget for the second phase. He said project officials have paid the contractor all but about $5 million. That money will be paid as work is completed.

“Getting an agreement is definitely very positive for the project,” said Stark, who on Wednesday is expected to brief board members of the Metropolitan Washington Airports Authority, the agency overseeing construction of the rail line.

Keith Couch, spokesman for Capital Rail Constructors, emphasized that the settlement covers only the previously announced delay. Couch is also expected to present his quarterly report to the MWAA board Wednesday.

After failing to reach a deal on their own, MWAA and the contractor used a mediator to settle the dispute, Stark said. The two sides split the $70,000 cost for that.

The Silver Line is one of the biggest infrastructure projects under construction in the United States. It is being built by MWAA and will become part of the region’s Metro system. It was broken into two phases in part because of cost concerns. The total cost is expected to be $5.8 billion.

The Silver Line’s first phase also was delayed. It opened in July 2014, six months later than anticipated, and was more than $225 million over budget. Even so, officials — particularly those in Fairfax County, who had lobbied for decades to have the rail line built — were eager to finally have Metro service in that part of the county. Many in Fairfax view the rail line as key to efforts to transform car-dependent, traffic-clogged Tysons into a walkable, urban oasis. There are four stops in Tysons Corner.

The second phase is expected to open in 2020 and, for the first time, will offer a rail link from downtown Washington to Dulles International Airport. It was first expected to be completed in 2018.

However, in fall 2014, project officials announced that they would have to redesign portions of the second phase to accommodate new state and federal regulations tied to storm water management. The design changes would affect the entire 11.4-mile line, which extends from Wiehle Avenue in Reston to Route 772 in Loudoun County.

The rail line is funded through a combination of state, federal and local dollars, but the majority of the project’s cost will come from drivers who use the Dulles Toll Road.