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The entryway to the Jay Street train station is going from eyesore — to sight for sore eyes.

Workers are finally painting ceilings on either exit on the west side of Jay Street between Willoughby Street and Myrtle Avenue, a Downtown disgrace that has languished through a decade of inexcusable neglect.

The Metropolitan Transportation Authority quietly launched the $250,000 job on the heels of a scathing summer report by this paper that found that the agency was spending $110 million to rehabilitate the subway station — but inexplicably excluded the disgraceful ceilings from its massive plans, which will be completed next summer.

But now, a section of ceiling closest to Willoughby Street is already completed, and on Friday, workers cordoned off a second section of the courtyard with plywood and plastic to prevent the spread of lead dust, scraping layers of paint that date back to the Giuliani administration.

The paint coat is cosmetic at best. A layer of plaster to fill in the bumpy topography was considered, but rejected because of its added cost, said Peter Heaven, a structural engineer with the agency.

Still, locals appreciate the work.

“Appearance matters,” said Michael Weiss, the executive director of the Metrotech Business Improvement District. “A neighborhood that looks like an eyesore tends to be shunned by people.”

Straphangers were not yet ready to embrace the agency.

“I’ve wondered why its been like this for so long because this area is getting gentrified,” said Tasha Guppara of Park Slope. “I’m surprised they let it go this long.”

The crummy courtyards are a part of 370 Jay St., a city-owned building that is leased to the MTA, which is responsible for its upkeep.

Heaven said that the hope is to get the job finished as soon as possible — in less than two weeks — so that straphangers can have access to all the exits.

“Time is of the essence,” he said.