The city was founded in 1883 by British explorer Henry Morton Stanley under the name Équateurville.

The headquarters of the Fourth Naval Region of the Navy of the Democratic Republic of the Congo are located in the city.

South of the Ngiri Reserve, a large area of swamp forest on the opposite bank of the Congo, it is located at the center of the Tumba-Ngiri-Maindombe wetland.

It is home to Mbandaka airport and is linked by a four to seven day trip by river barge journey to Kinshasa and Boende.

These plans included infrastructure for an estimated population of 100,000 people, a train station, a Catholic cathedral, a governor's residence, and a palace for future visits of King Leopold II of the Belgians.

Work was abandoned on the outbreak of the Second World War, and only the foundations of the bridge pillars remain.

In the 1930s, the Government of the Belgian Congo began several projects, including factories and a new city hall.

Near the end of the First Congo War in the late 20th century, hundreds of people (mainly Hutu refugees, women, and children) were massacred here on May 13, 1997.

A large research centre for Central African history, originally set up by Fathers Gustaaf Hulstaert and Honoré Vinck, is at the Catholic mission station of Bamanya (Congregation of the Immaculate Heart of Mary) (CCIM)), 10 km (6.2 miles) east of Mbandaka.

One of the finest botanical gardens of central Africa is at nearby Eala, about 7 km (4.3 miles) east of the town centre.