Jake Musga pleaded not guilty Wednesday and is being held on $2 million bail.
He was charged Wednesday with first-degree murder and rape of a child in the death of the boy, whose name has not been released.
Tacoma police arrested Musga at the Commencement Terrace apartments on Saturday after a witness called 911 to report that Musga was holding a baby "covered with bruises," according to court documents.
The child was rushed to a local hospital where he was pronounced dead.
Prosecutors say the toddler showed no signs of brain activity when he arrived at the hospital, was bruised "from head to toe," had internal bleeding and a blood-alcohol level of 0.12 -- an amount beyond what would be considered drunk in an adult.
Musga, who is not the child's father, told investigators he watched the child when the boy's mother was at work. According to police, he claimed the injuries resulted from a series of events on Thursday and Friday where the boy had accidents, such as bumping his head on a counter, slipping in the shower, and falling out of bed.
He also claimed he had poured himself a drink with multiple shots of vodka Friday evening and that the boy must have drank some while he was in another room.
But an autopsy revealed the boy had suffered injuries "too numerous to count," including fatal blows to the head and torso that were inconsistent with the events Musga described, prosecutors said.
According to court documents, the child's mother declined to speak with investigators.