Neither of the children were harmed during the approximately 15 minutes they were inside the vehicle at a retail parking lot on the Pickering Parkway at around 10:30 a.m.
One child is nine, the other is three months old. Durham police said the air conditioner was on and the children did not appear to be in distress.
Neighbouring Toronto is under an extreme heat alert and Environment Canada says the temperatures in the region are in the low 30s, but with the humidex figured in it feels more like 40 C.
The 38-year-old mother was issued two Provincial Offence Summons for leaving a child under 16 years unattended, under the Child and Family Services Act.
She was charged after a complainant noticed the two children alone and alerted authorities.
A funeral was held earlier this month for a two-year-old boy who died from heat-related causes after being left alone inside a car in Milton. The boy was in the care of his grandmother at the time. She was charged with criminal negligence causing death and failing to provide the necessities of life
A father was also charged this week in Oakville after leaving his nine-month-old daughter in a car for 15 minutes in a parking lot.