Rosdeep Kular, who appeared under her married name of Rosdeep Adekoya, is also accused of attempting to defeat the ends of justice.
The hearing took place in private and Kular, who made no plea or declaration, was remanded in custody.
Any trial would now need to take place within 140 days, unless the deadline is extended by the court.
Kular’s second appearance at Edinburgh Sheriff Court started shortly after 2pm today and lasted almost an hour.
The case was moved from court three to court 16, which is often used to hold judicial examinations. The Crown Office would not comment on the hearing.
However, it marked the start of the fiscal’s investigation into the death of Mikaeel, from Edinburgh.
The Crown Office now has 80 days to serve an indictment, including charges the accused will face in any trial.
Police Scotland are also continuing to investigate. However, so far no-one else has been arrested in connection with Mikaeel’s death.
Mikaeel was reported missing on 16 January by his mother.
The subsequent missing person appeal triggered a massive search with neighbours walking round the streets of Muirhouse and Drylaw shouting his name.
Many looked for the youngster throughout the night. The next day, police co-ordinated searches of the Cramond shoreline.
However, shortly before midnight on the same day, a child’s body was discovered in Kirkcaldy, Fife.
On Saturday, 18 January, police confirmed that a 33-year-old woman had been arrested and charged in connection with his death. At last week’s appearance, it emerged Ms Kular was facing a murder charge.
The Crown Office issued a brief statement today.
It said that no future dates were now scheduled for the case, and no further information would be released until the accused has been indicted and appeared in open court.