The station was originally built as East Jamaica in May 1885 and was renamed as Hollis in September of the same year.

[5][7] As part of the Metropolitan Transportation Authority's 2020–-2024 capital plan, the station will undergo extensive renovations – in addition to being made fully accessible-accessible.

[14][15] Work on the project was briefly paused in mid-2024 due to the temporary postponement of congestion pricing in New York City, which will help fund the renovations, but has since resumed.

The two middle tracks, not next to either platform, are used by through trains on the Port Jefferson, Ronkonkoma, Oyster Bay, and Montauk branches.

A fifth track south of the southern platform leads to the east end of the Hillside Facility and does not carry passenger service.