James Brennan's father, David Brennan, asked a babysitter to look after him for the night, but returned to his ground-floor maisonette in Chorlton-cum-Hardy, Manchester, the next morning and found his son dead.
Police said a man aged 25 had been arrested on suspicion of murder. He was detained 350 yards away outside a cafe 45 minutes after the body was found.
Mr Brennan was said to be "absolutely devastated".
Officers were trying to trace James's mother, who was believed to live in Northern Ireland.
He had been left with a babysitter on Wednesday night while Mr Brennan went for a night out in Manchester with friends.
Det Supt Martin Bottomley of Greater Manchester Police said: "The boy's father is very distressed and is being cared for by specialist police officers. He had left his son in the care of a family friend while he went out for the night and is absolutely devastated at what he found the next morning."
Det Supt Bottomley said that James - an only child - had been found in his bedroom.Reuse content