Born in St. Paul, Minnesota, Whelan received a Bachelor of Arts degree from the University of San Diego in 1961 and a Juris Doctor from the University of San Diego School of Law in 1965.

Whelan was a contracts administrator, planner and estimator for General Dynamics Corp. from 1961 to 1969.

As a superior court judge, Whelan presided over the infamous Betty Broderick trials in San Diego.

Whelan was nominated by President Bill Clinton on June 4, 1998, to a seat vacated by John Skylstead Rhoades Sr.

He assumed senior status on August 15, 2010. Notable cases that Whelan has presided over on the district bench include: