Leon Watson, 24, of the 2400 block of West Diamond Street, is charged with assaulting the 8 and 9 year old victims, who are brothers.
The boys also moved into Watson's home back in October, investigators said, but did not release any further details.
An anonymous tip led investigators to his home and he was arrested on Sunday.
The DA said Watson was a part-time coach for the Rhawnhurst Raiders football team from August through October of this year.
Officials with the Raiders say Watson was not an official coach. But in cell phone videos obtained exclusively by Action News, Watson can be seen with whistle in hand coaching the boys.
Mike Nitka is on the Raiders board of directors.
"He came up in August, tried to help out, he did helped out a couple of times, and he kind of just stopped coming around," said Mike Nitka.
And that's around the time, police say the two boys moved in with Watson at his North Philadelphia home.
Investigators say the boys' parents are estranged and looking for a place to live. Watson took them in and allegedly began sexually assaulting them.
"I thought they were his kids," said Eddie Ray. "But I guess they weren't his kids. They probably have no guidance, and this is the only person who took interest in them, and they relied on him for everything. It is shame he took advantage of them."
Officials with the Raiders say most of the coaches have been coaching for decades.
In the past, background checks were conducted, but they stopped in recent years.
Authorities say Watson also coached a team called the Little Vicks in North Philadelphia. They are urging parents to talk with their kids.
"It definitely gives me an opportunity to talk to my sons to talk about their coaches' good and bad touch, and that this type of thing happened," said Lynn Johnson.
The league says anyone officially coaching or even helping out will require background checks immediately.
The DA said investigators believe there may be more victims and is urging parents involved with Rhawnhurst Raiders or "Little Vicks" football teams to speak to their children. The investigation is ongoing.
Anyone with information is urged to call 9-1-1 or the Special Victim's Unit at 215-685- 3251.
The DA also said there is a phone line and email address to report sexual abuse. That phone number is 215-686-8019 and the email address is firstname.lastname@example.org.
Watson is currently being held on $500,000 bail.