Princess Elizabeth Primary School started as Bukit Panjang Afternoon School in 1952. It shared premises with Panjang Malay School and later with Chua Chu Kang Malay School. In 1954, the school moved to Princess Elizabeth Estate at Hillview Avenue and was renamed as Princess Elizabeth Estate School.
In 1986, Princess Elizabeth Estate School was renamed Princess Elizabeth Primary School and relocated to its present premises at Bukit Batok West Avenue 3. In 1989, the school celebrated its 35th anniversary. In 1994, the school celebrated its 40th anniversary. In 2012, the school celebrated its 60th anniversary. In 2015, the school became single-session.