The former New York Giants running back was "floored" by Tuesday's filing, according to the report, because it happened ahead of the couple's game plan.
A source told the website that Barber thought he and wife Ginny Barber had agreed that neither would file divorce papers "until after their babies were born."
She is currently eight months pregnant with twins. The couple also has two sons.
Earlier this month, Barber confirmed that he and his wife had separated after 11 years of marriage.
"This decision was a painful one, but we are moving forward amicably and will continue to work together to raise our children with the love and dedication they have always known," he said in a statement to the New York Post.
Reports at the time speculated that an affair with a former NBC intern may have contributed to the split.