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Prostějov was first mentioned as a village in 1141 (as Prostějovice) and obtained the rights of a town 1390. During the 14th century the town was enlarged and fortified. From the end of the 15th century Prostějov was a seat of the Bohemian Brethren who maintained a school and a printing house here. Later also Anabaptists settled in Prostějov. The opening of the first Austrian railway line, the Kaiser-Ferdinand-Nordbahn (see Bohumín) 1838–1846 initiated a period of industrial growth.

Prostějov is the birthplace of one of the most important architects of the Bohemia late gothic period, Matthias REJSEK (1450–1506), and one of the most important philosophers of the 20th century, Edmund HUSSERL (1859–1938), the founder of phenomenology.

Prostějov is well-known for its Art Nouveau and Secession style buildings which originated at the beginning of the 20th century:

The new town hall (nová radnice) [left] was built in 1911–1914. The tower has a height of 66 m.

The National Hall (Národní dům) [right] was built in 1908.