The minibus was parked at Craigroyston High School, where the charity is based, when it was set on fire around 5pm on Saturday – in broad daylight.
The vehicle, which belonged to the Muirhouse Youth Development Group (MYDG), was completely burnt out and is now unusable.
Dean Shanks, strategic director of MYDG, said the crime had an “immediate impact” on the work of the association.
The association generally takes groups of school children by minibus, but these excursions could not take place.
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MYDG began working at Muirhouse in 1977. According to Mr Shanks, the area has had problems with anti-social behavior in the past, but nothing as serious as this incident.
“It’s just insane, and especially to do it in broad daylight,” he said.
“Why would anyone do that? That’s the question we keep asking ourselves.”
The charity usually runs a summer program to take local children on residential trips, but those plans have been put in jeopardy.
While Mr Shanks hopes the charity will be able to buy a new bus in time, he is unsure if this will be possible.
Officers are currently working to investigate the incident.
A Police Scotland spokesman said: ‘We became aware of a burning van near Craigroyston High School on Pennywell Road in Edinburgh at around 5.15pm on Saturday 23rd April.
“The fire was put out by the Scottish Fire and Rescue Service and inquiries are underway to establish the cause of the fire.”