The sultan, dressed in military fatigues, prayed at the main Baiturrahman mosque in the provincial capital Banda Aceh shortly before embarking on a tour of the devastated city.
He was later expected to visit the island of Sabang, off the northern tip of Aceh province, where a 50-strong Bruneian military and civilian contingent are operating.
Though it shares an island with Indonesian territory, oil-rich Brunei was unaffected by the December 26 tsunami, which occurred thousands of kilometres (miles) away across the huge archipelago.
The disaster left more than 236,000 Indonesians presumed killed, most of them in Aceh.