Roderick Blacksmith was on trial for second-degree murder in the November 2008 death of 13-month-old Cameron Ouskan (OO'-skahn).
A Queen's Bench judge ruled the Crown did not produce evidence pointing to Blacksmith as being the person responsible.
Justice Deborah McCawley also said she is considering taking the rare step of having the Crown pay Blacksmith's legal costs.
The trial was told the young boy died from head injuries, but Crown witnesses could not pinpoint the day when the injuries would have occurred.
The Crown relied mainly on the fact that Blacksmith was the only adult in the home when the boy was rushed to hospital in Gillam, Man., but medical experts told the trial brain injuries can take days to develop.
"In my view, there is no evidence of an unlawful act, there is no evidence of Mr. Blacksmith having done anything wrong, and there is no evidence of a particular time frame," defence lawyer Saul Simmonds told court Friday.
Blacksmith's wife testified at the trial that she never hurt the baby, never saw her husband hurt the baby and never saw her biological children — four daughters between one and nine years old at the time — hurt the baby intentionally.
The trial heard the children would roughhouse with Cameron sometimes. As well, a babysitter had dropped the child on his head in a bathtub two days before he was rushed to hospital.
In a videotaped interview with police, Blacksmith said he put the boy to bed on Nov. 12, 2008, and when he went back to check on him, the baby was unresponsive and his mouth was filled with vomit.
Blacksmith told police he called the hospital and performed CPR and mouth-to-mouth resuscitation until help arrived.