The sixth-seed from Thornhill, Ont., wrapped up his 83-minute victory with a 10th ace to advance after playing last week in Bangkok and reaching the quarter-finals. He next plays Serb Viktor Troicki.
Raonic is playing at the ATP venue where he made his move onto the world stage in 2010. He has faced Rafael Nadal at the Ariake Coliseum in Tokyo in both of his previous appearances.
The Canadian now owns three match wins in Tokyo after his pair of second-round defeats against Nadal in 2010 and 2011.
"It was a good start for me, it was a chance to correct a few things that I didn't like about the way I finished in Bangkok (quarter-final loss last week to Jarkko Nieminen)," said Raonic. "This is a good sign for me.
"In the next round I hope to keep doing what I've been doing today. I need to play my game and stay aggressive. I want to play on my terms out there as much as possible."
Raonic was never threatened by Stepanek, breaking the 2010 Tokyo semifinalist to start the match, and needing three set points to close out the opener in 43 minutes.
In the second set, Raonic got on top 3-2 from his opponent's forehand error, then finished the morning encounter with an untouchable serve.
He now owns a perfect 3-0 record over Stepanek after defeating the Czech twice in 2011.
Raonic — the youngest player in the ATP top 20 at age 21 — won his 40th match of the season. He comes into the tournament ranked 14th in the world.