Blake Ross was reported missing from the Howdenhall area at around 3.15 p.m. on Saturday February 11.
Local officers launched a missing person investigation to trace the 13-year-old and he was subsequently discovered on a Lothian Bus at around 4 p.m. on Monday February 13, having taken unwell.
Blake was known to live with an underlying health condition and was taken to the Sick Kids Hospital where he sadly passed away at around 9 p.m. that evening.
His death is currently being treated as unexplained and inquiries are continuing.
Superintendent Lesley Clark of Edinburgh Division said: “This is a tragic death of a young boy and our thoughts are with Blake’s family at this very difficult time.
“In the coming days and weeks we will be working with our relevant partners to support his loved ones and provide them with alll the necessary support and assistance they require.
“Police Scotland has reported the circumstances surrounding the death of 13-year-old Blake Ross, who was reported missing from the Howdenhall area on Saturday, February 11, to the Crown Office and Procurator Fiscal Service.
“The matter has now been referred to the Police Investigations and Review Commissioner.
“As in all matters concerning police contact before death, we will provide any necessary assistance to the PIRC as they conduct their investigation and we await the outcome of their report.
“This is a tragic set of circumstances and thoughts and condolences are with Blake’s family and friends.”
The Care Inspectorate have been informed and there will be a multi-agency Significant Case Review, commissioned by the Chair of the Edinburgh Child Protection Committee, in accordance with our procedures.