Omer, originally known as Hevrona, was founded as a kibbutz in 1949. The early residents were demobilized Palmach soldiers. In 1951, it became a cooperative village known as Eilata. In 1953, it was re-established as a communal moshav by immigrants from Hungary and Romania and renamed Omer. The name is based on a verse from the book of Leviticus.
In 1957, residents of the ma'abarot in the vicinity moved to Omer. In 1962, it was renamed Tomer and became a neighborhood of Beersheba. Since 1974, it has been an independent town and suburb of Beersheba.