Asru’s mummified body had been on display in the Oxford Road museum’s Egypt and Sudan Gallery before it was moved into storage earlier this month.
She was mummified in a series of rituals used by ancient Egyptians to preserve the body after death in preparation for the afterlife.
Her remains and coffins were dug up in modern Luxor, the site of the ancient city of Thebes, before they ended up in the ownership of Manchester traders William and Robert Garnett in the early 1800s.
The body was donated to the Manchester Natural History Society in 1825 and placed on display for the next two centuries.
The museum spokesman said removing the display “reflects changes in how we think about our responsibility towards ancestors, museum collections and the communities they represent”.
He said: “Before making this change, we consulted with Egyptian colleagues, members of the Egyptian diaspora and visitors to the museum, helping us to understand people’s feelings about care for mummified people.
“However, the decision to remove Asru from display aligns most closely with what we understand about her own wishes,” the spokesperson said.
Asru’s final resting place has not yet been decided, with the museum now considering whether to keep her coffin and body in storage or return it to Egypt.