Spencer Lee Jordan, 26, and Marie Eve Magoon, 22, have each been charged with one count of second degree murder in the death Meika Dawn Jordan.
The six-year-old died in hospital on Nov. 14, one day after police were called to a Calgary home.
Police say family told them at the time that the girl suffered injuries after a fall down a set of stairs.
An autopsy concluded that she died as a result of multiple blunt force trauma.
Investigators said last week that the girl's father and stepmother had been suspects from the beginning, but new evidence narrowed down the timeframe of when the girl's injuries occurred.
"This has been a complex investigation utilizing a significant number of resources from within the Calgary police service. Resources from police and partnering agencies were also utilized," Staff Sgt. Doug Andrus told a news conference on Monday.
"This inter-departmental and inter-agency co-operation and assistance was key in resolving this case," he added.
Police said last week that the autopsy revealed that blunt force trauma was sustained to the girl's head and abdomen and was not consistent with a fall down stairs.
They also said she may have suffered other injuries prior to her death, including a third-degree burn to her palm and fingers. They alleged that at the time she suffered those injuries, she was in the sole care of her father and stepmother.
They said the two were uncooperative with the investigation.
Andrus said that Spencer Lee Jordan and Magoon were arrested Sunday without incident.
They will appear in court Tuesday.