Police and emergency services appealed to the public for help to find Hussein Al Mansoory, who was last seen running from Auburn Memorial Park towards the intersection of Station Rd and Rawson St about 10.30am on Saturday.
There were serious concerns for Hussein's welfare as he lives with Down syndrome and autism and is non-verbal.
Police confirmed the boy had been found "safe and well" just before 12.40pm on Monday.
Searchers had been experimenting with playing the 12-year-old's favourite music in the hope of drawing him out if he was hiding or sheltering due to his fear of strangers.
SES volunteers joined the search for 12-year-old Hussein Al Mansoory in the suburb of Auburn. (Dean Lewins/AAP PHOTOS)
State Emergency Service crews and police, including PolAir and the riot squad, were part of the search which focused on construction sites.
They believed Hussein could have taken shelter in one of the sites to escape the hot weather in Sydney during the weekend.
Temperatures at nearby Sydney Olympic Park had reached 28.8C at midday on Monday.
SES Auburn unit commander Jamie Newman said 70 volunteers searched until midnight on Sunday and almost 100 had joined the effort on Monday.
"We've got 20 teams from across the Sydney area and outside of the Sydney basin," he said.
"We've also got our specialist search and rescue team that will be searching the particular areas for the police today as well."
Superintendent Simon Glasser earlier said the boy had gone missing before but usually for much shorter periods.
"He is 12 years old, he's got special needs and he's been out and about by himself for 48 hours now so it's as high risk as it gets," he said.
"It's already at a critical point so we're throwing everything we have at it and we're going to keep searching."
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