The Museum was founded on 3 August 1893 by members of the Free Christian Church, based on Worthing Road. It is probable that the idea for a museum came out of the Shelley centenary celebrations of 1892, when the idea of a Shelley museum was mooted in the town although nothing came of the suggestion.

The Free Christian Church promoted education, debate and discussion among its members and already ran a library of some 15,000 volumes. The minister J.J. Marten and the Sunday School teachers proposed the creation of a museum "as a means of increasing knowledge among the young people," and a Museum Society was set up to promote collecting among its members and to offer talks and excursions to places of interest.

At first the Museum collection was displayed four times a year on church premises under the care of its first curator David Price, from 1893 until his retirement in 1920. The main focus of the early collections was natural history, geology and curiosities, and the Museum still has photographs of deformed potatoes and a hairless horse in its possession that were among its first donations.

In 1928 Park House, the former home of the Hurst family and the diarist John Baker, was sold to the Urban District Council and the old kitchen was made available to the Museum Society as a room for its first permanent display. The Museum opened at Park House on 27 September 1930 under its new curator, J.B. Shrewsbury (curator from 1929 to 1949) who was also art master at Collyer's School. With the outbreak of war in 1939 the Council needed more office space, meaning that the Museum faced the threat of being homeless. The Society was able to lease Causeway House from Captain Antony, where the displays occupied two rooms. At the end of the war Causeway House came up for sale. Horsham historian William Albery offered the town his large collection of documents and items from his Saddlery collection on condition the Museum was found a permanent home. West Sussex County Council bought the house and the Museum's future was assured on the Causeway.

In 1966 Horsham Urban District Council took over the running of the Museum and appointed curators to run it, rather than the Museum Society, and with the creation of Horsham District Council in 1974 the Museum became part of the new Council. The Museum displays expanded under Evan Perry's tenure as curator, between 1974 and 1983, including the erection of the eighteenth-century barn at the rear of the gardens. Perry's successor Elizabeth Kelly did much to improve storage conditions for the collections in the 1980s, and following the arrival of the Jeremy Knight in 1988 the Museum displays have been developed to include the entire building, as you see them today.

In 1999 the museum was awarded a Heritage Lottery Fund grant to improve storage, displays, cataloguing (including computers) and the fabric of the building. Since 2002 when the project finished the museum has continued to develop and in 2010 the museum opened a dedicated art gallery so Horsham Museum is now Horsham Museum and Art Gallery.