Officers entering the home Sunday night found the children, a boy and a girl, dead from stab wounds. The mother was rushed to a hospital, where her condition was not immediately known.
Officers arrived on what was described as a well-being check and entered by removing an air conditioner, said Boston Police Superintendent John Gallagher. The victims had multiple stab wounds.
"This is not a random incident. We are confident the neighborhood is still a safe neighborhood at this point," said Gallagher, adding that there were no arrests and no search for any suspects.
Police did not immediately identify the children, reported to be aged 10 and 12, nor the mother.
Friends and relatives said the woman had been distraught after recently losing her job at Children's Hospital.
"She was desperate," said Juan Gonzalez, a friend who came to the scene Sunday night.
Gonzalez said the woman never threatened to hurt her children, but told the Boston Globe that the woman had called his girlfriend Saturday night threatening to kill herself.
"She was a nice person, she was a good mother. She loved those kids so much," he said.
Gonzalez's girlfriend said the woman recently returned from a two-week vacation in Florida with the children and on Saturday threatened suicide, Monica Perez told the newspaper.
"She said she was giving up," Perez said.