In March 1935, Noonan was the navigator on the first Pan Am Sikorsky S-42 clipper at San Francisco Bay. In April he navigated the historic round-trip China Clipper flight between San Francisco and Honolulu, piloted by Ed Musick (who was featured on the cover of "Time" magazine that year). Noonan was subsequently responsible for mapping Pan Am's clipper routes across the Pacific Ocean, participating in many flights to Midway Island, Wake Island, Guam, the Philippines, and Hong Kong. In addition to more modern navigational tools, Noonan as a licensed sea captain was known for carrying a ship's sextant on these flights.