The Chapel was commissioned in 1623 for the Infanta of Spain, the intended wife of Charles I. It was completed in 1626-7 for Charles l's eventual Queen, Henrietta Maria of France, who used it as her private Roman Catholic chapel, bringing with her a bishop and priests from France as her chaplains.  Inigo Jones's plans included the gilding of twenty-eight coffers of the vaulted ceiling. Through small doors in the paneling of the west wall two of the original painted consecration crosses can still be seen.

During the Commonwealth the Chapel was probably stripped of its treasures and in 1650 a Council of State directed that it should he used as a library. In 1662, however, it was refurnished and restored as a place of worship bv Charles II for his Queen, Catherine of Braganza.  She appointed the Benedictine Father Huddleston who had hidden Charles II in his priest's hole after the Battle of Worcester (1651), to the Queen's Chapel and installed a community of friars of the Order of St Peter Alcantara in the Chapel's friary. Her coat of arms (the Stuart arms impaled with those of Portugal) can be seen over the east window and over the fireplace in the royal gallery and constituted part of the 1682 refurbishment undertaken by Sir Christopher Wren, Grinling Gibbons and Robert Streater.  Most of the interior of Queen Catherine's chapel has survived.  Subsequently it was used by Mary of Modena, the second wife, and Queen, of James II.

In 1689 the Chapel was closed but around 1700 William III granted it for Reformed worship by French- and Dutch-speaking congregations; later, Queen Anne established a German Lutheran Royal Chapel in a room in Great Court.  George III married Charlotte of Mecklenburg-Strelitz in the Queen's Chapel in 1761.  In 1781 the use of the two chapel buildings was exchanged and the Queens Chapel became known as the German Chapel Royal: the smaller chapel was destroyed by fire in 1809.  From 1880 until 1936 the Queen's Chapel was used by a Danish Lutheran congregation who erected a tablet to the memory of Queen Alexandra.

After Queen Mary came to live at Marlborough House in her widowhood, the Chapel was restored bv the then Office of Works.  The restoration included the remodeling of the reredos to accommodate the altar-painting of The Virgin and Child with SS Joseph, John the Baptist and Catherine, ascribed to Annibale Carraeci and acquired bv Charles I.  The organ - originally built by James Snetzler in 1760 for George III for the private chapel at Buckingham House and given to the Queen's Chapel in 1830 - was also rebuilt.  In 1938 the Queen's Chapel was given to the use of the Chapel Royal, St James's Palace. All services from Easter Day until the last Sunday in July each year are held here and are open to visitors.