Police said 29-year-old Thomas Smith told them he woke up from sleeping downstairs and found the kitchen on fire and fled the house.
He said he attempted to re-enter the house to rescue his two children, 3-year-old Michael Smith and 2-year-old Jasmine Smith, but was unable to.
At least three fire fighters rushed into the burning home to rescue the toddlers from an upstairs bedroom where they were sleeping.
"Your adrenaline just starts rushing and you do what you're trained to do, put the fire out and search and rescue," Capt. Greg Brook said.
Officials told Eyewitness News that the siblings suffered life-threatening injuries and were transported first to Wake Medical Center and then to the UNC Jaycee Burn Center.
Garner EMS Chief Bill Frederick said on the way to the hospital one child suffered cardiac arrest and had to be revived.
Saturday afternoon, the children's mother said Michael was having difficulty breathing, but Jasmine was recovering. Both kids have burns on their face, arms and legs and are in critical condition.
Neighbor said they felt helpless observing the aftermath.
"I could not imagine being in that position," neighbor Brenda Smith said. "My heart really goes out to them. Its nerve wrecking to know your child is in the house knowing you can't get in there to get to them.
The fire caused damage to both sides of the duplex, but residents from the other side escaped uninjured.
An investigation by the Wake County Fire Marshal's office found that the fire started in the kitchen and appeared to be accidental. Officials said a final report on the cause would be available next week.