The man, 25-year-old Trevor Braymiller, is considered armed and dangerous, Sedro-Woolley police Chief Doug Wood said.
"He's been in the area for quite some time," Wood said. "He's a convicted felon with a prior conviction for selling drugs," Wood said.
Initial reports Sunday morning said the boy had shot himself with a gun, Wood said, but after a medical examiner looked at the boy, it was determined that was not the case. Wood said investigators are treating the case as a homicide.
Braymiller is believed to be moving on foot, with officers from several law enforcement agencies chasing him. Wood described Braymiller as having "scruffy" facial hair and wearing a red or orange shirt.
On Sunday afternoon, officers were focusing the search on the Big Lake area, just south of the town, Wood said.
Investigators say a police dog found the gun believed used in the shooting at a nearby church, but Braymiller is still on the run.
Braymiller's friends told KOMO News they believe Braymiller left because he was distraught over the boy's death and wasn't supposed to have a gun.
"I'm sure he's thinking something horrible has happened and doesn't know what to do," said Reuben Deyer.
Deyer says Braymiller called him for a ride Sunday morning.
"He said he went outside in the garage to smoke a cigarette and he heard a boom," Deyer said. "And went back in the house and his son wasn't moving."
"He's not supposed to be around guns," Deyer said. "Probably why he's going."
Another friend told KOMO News he was staying overnight in Braymiller's home.
"What woke me up was a gunshot and then I heard everybody frantically yelling," Danny Brown said.
Brown says yes, Braymiller had two guns but can't imagine Trevor harming the little boy.
Police say only Braymiller can explain exactly what happened in that house. They hope he turns himself in, or at least cooperates when officers find him.
"We don't want anything else bad to happen," said Lt. Lin Tucker with Sedro-Woolley police. "We don't want anything bad to happen to him."
Investigators believe Braymiller was not the boy's father, but rather a father figure. He also has a 1-year-old daughter.
The boy's mother was questioned and is now with her family. The boy was transported to Skagit Valley Hospital and was pronounced dead.