Phelps appeared at the Charlotte UltraSwim Grand Prix and won both the 200-meter freestyle and 100-meter butterfly in dominating fashion.
He had not competed since winning a record eight gold medals at last summer's Olympics in Beijing.
Since then, a photograph showing him smoking a marijuana pipe landed him a three-month suspension by USA Swimming, the sport's national governing body.
He turned in a time of 1:46.02 in the freestyle and then won the butterfly in 51.72.
"I wanted to come back and do something respectable in the pool," Phelps said. "The next few weeks are going to be really important in my training. It didn't matter how I felt tonight, I was just excited to race. That's what is important, that I still have that passion to race."
Phelps, 23, has won 14 Olympic gold medals overall. He will return Saturday to compete in the 50-meter freestyle and 100-meter backstroke. Phelps will finish his weekend with the 100-meter freestyle on Sunday.