The remains, known only as "Burial 159", show signs of the child having her bones broken repeatedly, and being shaken repeatedly, the Daily Mail reported.
Experts say the case may stem from an ancient Egyptian belief that children had to be "toughened up" as they grow.
The discovery was made by researchers at a cemetery in Dakhleh Oasis.
Sandra Wheeler, a bio-archaeologist at the University of Central Florida who led the team, said researchers found a number of bone fractures throughout the body, including the forearm, ribs, pelvis and back.
One fracture on the child's upper arms was in the same spot on each arm, and showed a break all the way through - which experts say would require a large force.
The researchers believe that someone grabbed the child's arms and used them as handles to shake the child violently.
The archaeologists are not sure what ultimately killed the toddler.
The research will be published in an upcoming issue of the International Journal of Paleopathology.
The Dakhleh Oasis is one of seven oases in Egypt's Western Desert. The site has seen continuous human occupation since the Neolithic period, making it the focus of several archaeological investigations, said Wheeler.