Anthony Blake Viles, 27, of Pocatello is being charged in the death of his son, 6-year-old Afton Allison.
The Bannock County Prosecutor's Office made the announcement at 11 a.m. Tuesday.
Deputy Chief Prosecutor Vic Pearson said that when a child under 12 dies as a result of aggravated battery, it automatically becomes a case of first-degree murder.
Viles was originally held on felony charges for injury to a child after prosecutors said he admitted to striking Afton last week.
Afton died Sunday.
At a Pocatello news conference Tuesday, Pearson said there was no indication of a specific weapon, but that the boy had suffered a large injury to the head. The prosecutor's office is awaiting more detailed medical reports from Salt Lake City.
"Ultimately, we?re talking about an individual that just passed away two days ago, so we?re relatively quick in this process," said Pearson. "But we?re looking into those particular questions, and trying to get to the bottom of all the facts so we know exactly what going on with this young individual."
Viles was arraigned Tuesday afternoon. He participated in the proceedings by video from the Bannock Jail. Bail was set at $1 million.
Afton's mother and stepfather watched the arraignment. Stepfather Jared Wrigley said it's good for the family to see justice being done.
"It does make us feel a little better that the community is free of one less scumbag," Wrigley said.
His preliminary hearing is scheduled for April 26, though scheduling depends on when the results from the medical tests come in.
The child?s death has hit the Pocatello community hard. On Monday night, more than 50 people showed up at a candlelight vigil to remember Afton, some of whom did not know him.