The inquiry comes after Keane, a pupil at Liberton High School, died when a modesty wall in a changing room collapsed on the morning of April 1, 2014.
Parties involved in the inquiry yesterday attended Edinburgh Sheriff Court, where preparations were discussed before Sheriff Principal Mhairi Stephen QC.
A further preliminary hearing will be held on April 13 after which the inquiry is expected to get under way on June 5.
Last year it emerged that no-one would be charged over the schoolgirl’s death following an investigation by the Crown Office into the tragic incident.
It was a move welcomed by Keane’s father, Clark Bennett, who previously spoke of his relief at the decision.
Mr Bennett, who now lives in Inverness, told the Evening News at the time that his family hadn’t wanted to endure a criminal trial and instead wanted to focus on trying to rebuild their lives.
He said: “I knew it was never going to happen. And now the Fatal Accident Inquiry will be starting.
“The outcome of the FAI will hopefully give Keane’s mum and me a way to know exactly what happened that morning.
“This decision has given myself and the rest of my family a bit of closure.
“I have been dealing with the police and my lawyer every second day, how can I move on with that going on?”
The case was investigated by police and the Health and Safety Executive under the direction of the Crown’s health and safety division.
The Crown Office added a criminal ruling could still be reconsidered if new evidence over the circumstances of Keane’s death came to light.
Hundreds of tributes flooded in after the 12-year-old’s death three years ago, with a song recorded by friends in her memory making it into the top 100 on the download chart in December 2014.
Last year Keane’s mother, Abbie Wallis, spoke of her hope that the inquiry’s would lead to changes in the way school buildings are structurally monitored.
She said: “If they hadn’t decided to hold an inquiry, it would have felt like Keane wasn’t important enough to look into what happened.
“I hope lessons will be learned regarding how school surveys are carried out and money prioritised.
“Now, whatever plans will be put in place, people will think ‘that’s because that little girl died’.
“My biggest fear is that people will forget her. This way she will always be remembered.”
She added: “I am dreading the detail coming out as it puts pictures in your head.
“There are probably certain things I won’t want to know and I may choose not to hear.”
As well as investigating the circumstances surrounding Keane’s death, the probe will also examine the safety of internal freestanding walls.
Liberton’s gym hall has since been demolished on the wishes of school staff and parents.
The city council said it would co-operate fully with the inquiry.