El Paso police said around 7:30 a.m. Friday, that the children were found safe and unharmed.
The suspect, Miguel Mendez, was taken into custody, said police.
The Texas Department of Public Safety said the children were taken with their mother Brenda Estrada.
The children are identified as Brandon and Ashley Estrada.
El Paso Police said the children's mother is pregnant and was held at gunpoint when they were taken by Mendez.