Pennington was given his junior international debut in 1998 at an ISU Junior Grand Prix event in Sofia, Bulgaria, where he placed 4th, and then placed 9th in his second assignment, in China. Since the 1999 World Junior Championships were scheduled to be held before U.S. Nationals, he competed at a since-discontinued competition to determine the US team. He placed third and was sent to Junior Worlds, finishing 16th. At the 1999 Nationals, Pennington won the bronze medal on the junior level. In 1999, Pennington was given two Junior Grand Prix events and placed 5th at both. He then won his Sectionals and won the junior silver medal at Nationals. This earned him another trip to the Triglav Trophy, where he won gold on the junior level.