The monarch and the Duke of Edinburgh toured the Chelsea attraction which is set to open to the public later this month after a three-year £23.75 million revamp.
It was founded in 1960 by Royal Charter and established to collect, preserve and exhibit objects and records relating to the land forces of the British Crown.
Now the Chelsea-based museum has been transformed into five bright thematic galleries.
The exhibitions include soldier, army, battle, society and insight and provide a space to explore and discuss the British Army and its relevance to society from fashion and films to flood defences and conflict.
On display will be the Queen's own uniform from when she held the honorary commission of Brigadier in the Women's Royal Army Corps (WRAC) from 1949 to 1953.
The museum acquired the uniform in 1993, following the disbandment of the WRAC in 1992.
In the attraction's cafe area the Queen, clad in a pale blue coat and hat, and the Duke met donors and museum staff before the monarch unveiled a plaque to mark her visit.