The vast collection at the museum traces its origins back to 1738. During that year King Charles VII of Naples and Sicily (later Charles III of Spain) decided to build a hunting lodge on the Capodimonte hill, but then decided that he would instead build a grand palace, partly because his existing residence, the Palace of Portici, was too small to accommodate his court, and partly because he needed somewhere to house the fabulous Farnese Collection which he had inherited from his mother, Elisabetta Farnese, last descendant of the sovereign ducal family of Parma.
Over the years, the palace was enlarged and filled with more art. In 1787, on the advice of Jacob Philipp Hackert, a laboratory for the restoration of paintings was created.
When the Parthenopaean Republic was declared in 1799, King Ferdinand IV fled to Palermo on board Nelson's Vanguard, taking the most valuable items from the museum with him. What remained was looted by the French troops of General Jean Étienne Championnet who were billeted there during the short life of the Republic in 1799. Later on, during the nine years of French reoccupation (1806 to 1815), the art collection was transferred to the Naples National Archaeological Museum. When King Ferdinand returned from Sicily in 1815, he employed many painters and sculptors to work on the redecoration of the palace. It was finally completed in 1840, and a gallery housing contemporary art was added.
After the palace passed in 1861 to the House of Savoy, further pieces were added to the art collections, appointing Domenico Morelli as consultant for new acquisitions. They also added an extensive collection of historic firearms and other weapons. In 1866, the boudoir of Maria Amalia of Saxony was transferred to Capodimonte from the Palace of Portici, and in 1877 a Roman era marble floor was brought in from a Roman villa on Capri.
After the end of the monarchy, the palace became purely a national museum in 1950, with many of the exhibits being returned from the National Museum.
Elsewhere in the palace, the royal apartments are furnished with antique 18th-century furniture and a collection of porcelain and majolica from the various royal residences