The Botswana Public Employees Union has a long history as a labour organization. It started as staff association as far back as 1942, then known as Bechuanaland Protectorate Junior Civil Service Association. It co-existed alongside its counterpart, Bechuanaland Protectorate European Senior Civil Service Association.
It was not until the 1960s when the two organisations merged to form Bechuanaland Civil Service Association (BCSA), which after independence, transformed into the Botswana Civil Service Association. The association went through another transformation process in the 1990s’ when it was now called Botswana Civil Servants Association. In 2007 , the Association underwent another transformation, culminating with it's attainment of a Trade Union status to be known as the Botswana Public Employees Union.