Walter William Rosario, a 40-year-old priest and school headmaster, went missing on Monday from a village in northern Bangladesh where suspected Islamist extremists last year hacked a Catholic grocer to death.
His disappearance followed a rise in Islamist extremism in the Muslim-majority country, where at least three Christians, including two converts from Islam, have been hacked to death in recent years.
Police said Rosario had been found in the northeastern city of Sylhet, adding the disappearance was likely for personal reasons.
The news came as Pope Francis met with Rohingya refugees in Dhaka at the end of a visit dominated by the plight of the Muslim minority who have fled ethnic unrest in Myanmar and taken refuge in Bangladesh.
Christians make up less than 0.5 per cent of Bangladesh's 160 million people.