The long-delayed Fenway Center development over the Massachusetts Turnpike is now closer than ever to launching construction, thanks to a plan to do the easy part first.

The board of the Massachusetts Department of Transportation Monday voted to let developer John Rosenthal build two apartment buildings on land he owns alongside the Turnpike near Fenway Park, before building a costly deck over the Pike itself for a 27-story tower with 335 more units that could help remake the neighborhood.

Rosenthal first pitched the complex project about 15 years ago and has pushed it through lawsuits, a huge recession, various investors and partners, and multiple state administrations. He also privately managed renovations of the MBTA’s Yawkey Center commuter rail station, laying the groundwork for a project that relies heavily on public transit.

Now he has investors, a partner in veteran housing developer Gerding Edlen, and a plan to break ground in September.

“We’re looking forward to it,’’ Rosenthal said Monday.

Over the last year, he has been hashing out a deal with state officials to break up the $600 million project into two phases, starting with a pair of apartment buildings — 313 units in all — on firm ground at the corner of Beacon and Maitland Streets, across the Turnpike from Kenmore Square. In exchange for being allowed to delay the deck over the Turnpike, Rosenthal agreed to pay $21 million to the state before construction starts on the first phase.

Then he hopes to use the positive momentum to attract investors to help finance the deck and larger-scale development over the highway.

Transportation Secretary Stephanie Pollack said state officials were persuaded by that argument.

“It’s extraordinarily difficult to do development over air rights, and by having the project proceed into two phases we get a big chunk of the project going, on the non-air rights part that’s easier,’’ she said. “And that hopefully increases the possibility that we can make the air rights happen later.’’

The MassDOT board vote on Monday approved the $21 million, 99-year lease for the first phase of the lease, which will be formally executed by the end of September.

For the portion above the Turnpike, the state will negotiate the terms of the lease by the end of 2020, based on market rates.

If the developers don’t start construction on the second phase by the end of 2020, Rosenthal and Gerding Edlen will owe the state a $3 million penalty.

“We fully expect to get to phase two,’’ Rosenthal said. “But frankly we can’t get to phase two without starting on phase one.’’

If they do, they will have pulled off the first project to successfully build atop the Pike in Boston since Copley Place opened in the 1980s.

Adam Vaccaro can be reached at adam.vaccaro@globe.com. Follow him on Twitter at @adamtvaccaro. Tim Logan can be reached at tim.logan@globe.com. Follow him on Twitter at @bytimlogan.