Kyle Wood, from Tranent, East Lothian, was found dead on Monday after suffering a suspected seizure in his sleep.
Just six days earlier the 14-year-old had discovered he would take part in the baton relay ahead of the Glasgow Games.
A Police Scotland spokesman confirmed they had been called to the Ross High School pupil’s home, where he lived with his parents and sister, but added that it was a medical matter and there were no suspicious circumstances.
Following Kyle’s death, his father, Scott, 38, had posted on Twitter: “Just like to say thanks to everyone who has sent me their condolences on what has been the worst day of my life #sleeptightson.”
Dozens of tributes have poured in for the 14-year-old, who was an avid Hearts fan.
The baton, which tours the Commonwealth nations, enters the country on 17 June as part of its trip around Scotland.
The East Lothian leg of the journey starts in Musselburgh and ends in Haddington and Kyle would have carried the baton on part of the route.
Earlier this month Mr Wood had shared the news that Kyle had been picked for the relay on social media.
He tweeted: “So proud of my wee man getting chosen to carry the Commonwealth Games baton. He is so excited to have been chosen. Well done Kyle.”
Glasgow 2014 boss David Grevemberg was among those who paid tribute to the teenager yesterday.
He said: “Our thoughts are with Kyle’s family at this difficult time, and on behalf of the Glasgow 2014 Commonwealth Games we offer our heartfelt condolences.”
Paul Reynolds, headteacher at Ross High School, said that being chosen to carry the baton had been a “much deserved honour”.
He added: “Kyle was a great boy and very well-known and liked across the school. He was an all-rounder but particularly enjoyed sport.
“He made a big contribution to the life of Ross High School. Kyle will be sadly missed and I would like his family and friends to know that we send them our deepest sympathies. Things won’t be the same without him.”
The teenager’s friends took to social media to post tributes.
Suzanne Hendry, wrote: “Shocked to hear this sad news. Thoughts and prayers are with Kyle’s family.
“Now sleeping with the angels and yer Grandad wee man. RIP Kyle.”
David Archibald wrote: “Aw man I still canny take it in. RIP wee guy.”
Hearts Women and Girls team were among those to post their condolences.
They tweeted: “Rest in Peace little Kyle. You brought a smile to so many faces at the club. Far too young to be taken away. You will be deeply missed.”