Police confirmed the development during a press conference earlier this evening.
The woman is expected to appear at Edinburgh Sheriff Court on Monday.
Police Scotland Assistant Chief Constable Malcolm Graham, who spoke during the press conference, said: "During the course of today, the investigation into the disappearance of Mikaeel Kular has continued at pace.
"Following formal identification, I can now confirm that a 33-year-old woman has been arrested and charged in connection with Mikaeel's death.
"The woman is expected to appear at Edinburgh Sheriff Court on Monday."