Construction crews have punched through a 100-year-old rail tunnel in the LIRR’s Vanderbilt Yard as part of ongoing work to modernize the Brooklyn storage facility.

Underneath congested Downtown Brooklyn streets, the 4-foot-thick concrete wall of the tunnel was blasted open this summer to build a direct train path between the yard and Atlantic Terminal for the first time.

The connection will be known as the “West Portal,” one of several operational enhancements that Greenland Forest City Partners, a joint venture between developers Greenland and Forest City Ratner, are delivering to the yard as part of a real estate deal to build part of its $5 billion Pacific Park project above the facility.

“We were surprised by the condition of the wall; it was remarkable how well it still stood,” said Michael Gagliardi, project manager at Forest City Ratner, during a recent tour of the LIRR yard’s 8.4-acre storage site sitting between Pacific Street and Atlantic Avenue.

“I guess, with concrete they built pyramids — and they’ve lasted a pretty long time too,” he joked. “This was our pyramid.”

The new portal, when complete, will increase accessibility for all LIRR trains terminating in Brooklyn. The empty trains have had to backtrack east about a half-mile into the Atlantic Avenue rail tunnel, come to a full stop, and then return west to access the rail yard for servicing and storage before being put back into service.

That process blocks other trains from using the tunnel for six to eight minutes at a time, which adds up to about two hours of wait time each day, according to the MTA.

The upgrade was a condition in the MTA’s deal to sell the air rights to the developers for Pacific Park, the 22-acre, mixed-use commercial and residential space formerly called “Atlantic Yards” that, after several delays, will be built over the next decade.

Along with the portal, crews will install electric signals to replace manual counterparts. Sewer connections will be built out from one to all nine of the yards’ tracks. The enhancements will also give MTA staff more space to navigate train cars.

“As far as the service of the trains in the yard, whether it’s an overhead platform, or widened aisles or toilet cleaning — everything that helps our crews and maintenance is going to then sift down to benefit the customers as well,” said MTA spokeswoman Meredith Daniels.

The refurbishing will transform the facility from antiquated to “state-of-the-art,” according to the MTA. The project is on pace to meet its December 2017 completion date. After then, the developers will begin working to build a street-level platform on top of the yard to support the megaproject planned above.