The unit, named after Madonna's Malawi-born daughter, Mercy James, is the first of its kind in the country, reported Variety.
The child care unit is funded by the 58-year-old singer's charity Raising Malawi in collaboration with the minister of health.
"When you look into the eyes of children in need, wherever they may be, a human being wants to do anything and everything they can to help, and on my first visit to Malawi, I made a commitment that I would do just that.
The new wing will help Queen Elizabeth hospital double the number of surgeries performed on children each year, while also serving as a training center for local doctors in Southern Africa.
"Malawi has enriched my family more than I could have ever imagined. It's important for me to make sure all my children from the country maintain a strong connection to their birth nation, and equally important to show them that together, humans have the power to change the world for the better," Madonna added.