The 22-year-old has been charged after police claimed a four-month-old boy was the victim of shaken baby syndrome north of Brisbane in early 2024.
The infant had been airlifted from Bundaberg to Brisbane's Queensland Children's Hospital about 5.18pm on February 27, 2024, police said.
The boy passed away in hospital on March 3.
The man was arrested on Friday night following a "meticulous and challenging" police investigation, Detective Inspector Wade Lee said.
"It will be alleged the injuries are consistent with what is commonly known as a child's shaken injury," he told reporters in Bundaberg on Monday.
Police allege the injuries occurred at a Bundaberg West home in late February 2024.
The man allegedly had a "family relationship" with the boy but Det Lee did not go into details.
The boy's family was known to Child Safety before the tragedy, he said.
Asked if police had spoken to the boy's father, Det Lee said he "could not get into that".
The mother is assisting police with enquiries, he said.
Asked why it had taken so long for charges to be laid, Det Lee said: "The investigation of a child's death is a particularly difficult investigation for a number of reasons.
"There are complexities around a child dying."
Det Lee said the charges "largely relied upon medical evidence".
The man has been charged with murder and torture, both domestic violence offences.
He was set to appear in Bundaberg Magistrates Court on Monday.
Det Lee said bail would be opposed.
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