State Supreme Court Justice Jerry Garguilo made the ruling after Debra Baker of Coram, N.Y., told the court she is moving to Venice, Fla. The unemployed bookkeeper explained her house is in foreclosure.
Garguilo ordered the Bakers' children, 6 and 9, to communicate three times a week with their father on Long Island using the video-conferencing program.
James Baker's attorney is considering an appeal because his client doesn't know how to use Skype.
A national divorce center says Skype visitations are uncommon but not unprecedented.
The decision was published this week in the New York Law Journal.