Irene Brennan says her thoughts are with Mikaeel's family at this tragic time, particularly his brothers and sisters.
She is the head teacher of The Flora Stevenson Primary School in Comely Bank Road, Edinburgh, where Mikaeel was a pupil in the nursery class.
She says staff have been taking advice from psychological services ahead of children returning to school tomorrow.
The letter to parents says: "I am sure you will recognise that this is an extremely difficult time for everyone at the school but we are determined to work together to support our pupils over the coming days.
"Over the weekend I have met with my deputes, teachers and all nursery staff to discuss how we would manage things and we are receiving advice and guidance from the Children and Families Psychological Services Team on the approaches we can take to support our children."
She also thanked parents for supporting her and her staff.
Mikaeel's remains were found in woodland in Kirkcaldy, Fife, late on Friday night.
His mother has been arrested in connection with his death.