Rosdeep Adekoya, 34, was also charged with attempting to defeat the ends of justice when she appeared before judge Lord Boyd at the High Court in Edinburgh.
The Crown allege that she murdered her son after assaulting him on various occasions between January 12 and January 15, 2014.
Prosecutors also claim she lied to police officers investigating her child's disappearance.
Adekoya, whose address was given as Cornton Vale Prison in Stirlingshire, did not enter a plea during the two minute long hearing.
She was dressed in black, wore glasses and sat beside two security officers.
Adekoya, originally of Drylaw, Edinburgh, was arrested following claims that her child disappeared from her home in the city in January.
Members of the local community helped police search for Mikaeel shortly before his body was discovered in woodland in Fife.
Prosecutors allege Adekoya assaulted her three-year-old son by repeatedly seizing hold of him and punching him on the head and body.
It is claimed that her actions caused his body to strike against a hard object and that she inflicted blunt force injuries on his head and body. It is also claimed she failed to seek medical attention for him and that she murdered him.
The case will next call at the High Court in Edinburgh on July 25.