The magnitude 7.6 quake killed 241 people. Four are still missing. More than 9,000 residents whose homes were destroyed or damaged are still living in evacuation facilities such as community centers and school gymnasiums.
Reconstruction has come slowly in a largely rural area with an aging population. The region is known for Wajima lacquerware and other handicrafts.
Hundreds of people lined the streets to cheer the imperial couple and held up their phones to take photos of them waving back from the window of a bus.
Naruhito and Masako had not visited earlier because they did not want to interfere with the immediate relief and reconstruction efforts, officials said.
In Wajima city, where 102 people were killed, the royal couple were escorted by Mayor Shigeru Sakaguchi on a visit to more than 100 people still taking refuge inside a community center.
The couple knelt on the floor — a gesture started by his parents to get closer to the people — and talked to the residents, asking about their health and other difficulties.
They also stopped by the burned down ruins of a popular morning market, where 10 people perished. The couple bowed deeply and prayed in silence.
Sakaguchi said their warm words inspired him and the residents to keep up the reconstruction work despite slow progress.
The couple also visited evacuees in a gym in the town of Suzu.