The province used to have a program but it was shut down in the late 1990s following the deaths of 12 babies and a $2.4 million inquest that found several of the children's deaths were preventable.
Manitoba Health says there aren't enough children with serious problems to bring the program back.
Dr. Reeni Soni, head of pediatric cardiology at Children's Hospital, tells CTV Winnipeg that right now about 150 children a year in the province need heart surgery.
She says for the province to have its own program, that number would have to be closer to 250 or 300.
But the families of sick babies say they'd rather their children be able to get treatment closer to home.
One-year-old Oliver Hilder Titarniuk has a number of conditions, including two holes in his heart that needed specialized treatment in Edmonton.
"He's been stronger than me and Samantha have been," said Oliver’s father, Steven Titarniuk.
Oliver’s parents had to drop everything, including Titarniuk’s job, to go to Edmonton and stay in a hotel while the little boy was being treated.
"We had less than 24 hours’ notice," said Samantha Hilder, the boy's mother. "We had to leave and we were gone for two full months with kind of no expectation of when we would be coming back.
"Right now we're waiting for him to get strong and big, they'll then fix his heart."
Manitoba Health did pay for travel, hotels and even meals for both parents to be with Oliver.
Soni said the right place for children such as Oliver is in Edmonton.
"I think the general sense across the entire country is that to get the best long-term consistent results, it's better to centralize those kinds of operations to a few places across the country so those centres are doing lots and lots of cases to maintain their skill," she said.