Original inhabitants of the area between Parsonage Creek near Oceanside and Milburn Creek near Freeport were Native Americans known as Merokes, or Merrick, an Algonquian tribe indigenous to most of the South Shore of Long Island, who lived in two villages along Milburn Creek. In 1643, the land became known as Hick's Neck after two of Hempstead's early settlers, John Spragg from England and John Hicks from Flushing, who extended Hempstead village south to the salt meadows. The grist mill built by John Pine in 1686 on Milburn Creek attracted more settlers who engaged in fishing, farming, marshing, raising longwood, and breeding and raising sheep. Between the American Revolutionary War and the War of 1812, growing Hick's Neck came to be called the village of Milburn. The first churches were built in 1810 and 1872, and the first school was built in 1833.
After the area was previously regarded as Hick's Neck and later Milburn, Baldwin was founded in 1855 (as Baldwinsville) and named in honor of Thomas Baldwin (1795–1872), who was a sixth generation member of the Baldwin family of Hempstead and the leading merchant of Milburn at the time. Mr. Baldwin owned a general store named T. Baldwin and Sons, as well as a hotel at a location that would now be considered the northwest corner of Merrick Road and Grand Avenue. Mr. Baldwin also owned and operated a sawmill by Silver Lake just southeast of the hotel.
In 1867, the South Side Rail Road began operating with a station in Baldwinsville. In 1870, one of Thomas Baldwin's sons, Francis Baldwin, became a member of the New York State Assembly representing Queens County's 2nd District and, then later, he served as the Queens County treasurer. (During this time, Baldwinsville was part of Queens County.) A year later, the name of the village was changed from Baldwinsville to Baldwins by the U.S. Postal Service so as to not confuse it with the village of Baldwinsville in upstate New York. By 1892, by an act of local government, the village was officially named Baldwin.
Shortly after Hempstead separated from Queens County in 1899, people began to move to "Beautiful Baldwin", as it was called by Charles Luerssen, a village realtor, for the village's fine boating, bathing, and fishing. By 1939, ten years after the opening of Sunrise Highway, Baldwin became the largest unincorporated village in New York State—a title that was lost to Levittown by 1960.
In 1990, the area south of Atlantic Avenue was designated as Baldwin Harbor,a hamlet (and census-designated place) with the 1990 United States Census. Baldwin Harbor remains a part of the town of Baldwin's postal code, and school district and library system.
In May 1910, near what is currently known as Plaza Elementary School on Seaman Avenue and Rockville Drive in Baldwin, a breakthrough in American aviation history was made. The first all-American monoplane was designed, built, and successfully flown at this location by brothers Arthur and Albert Heinrich. In the plane's initial and subsequent models, its unique designs featured controls that were combined into one stick which allowed the pilot to fly the plane using one hand.
The name of the area was officially called Baldwin in 1892 while the area was still in Queens County. In 1899 Nassau County was established which encompassed the Town of Hempstead and it's several villages and hamlets including Baldwin.
Through the years Baldwin has also been known as:
Baldwin is located at (40.663346, -73.610618).
According to the United States Census Bureau, the village has a total area of , of which 0.34% is water.