It is the first papal visit since the end of the war in 2009 that saw the army and rebels accused of atrocities.
On Tuesday, the Pontiff called for the "pursuit of truth" to promote "justice, healing and unity" in the nation after years of civil war.
Last week Sri Lankans elected a new president, Maithripala Sirisena, ending 10 years under Mahinda Rajapaksa.
Pope Francis is in Asia on a six-day tour. He will next travel to the Philippines.
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Yogita Limaye: The Pope's trip comes at a significant time for Sri Lanka
On Wednesday the leader of the Catholic Church will celebrate a Mass in Colombo where he will canonise Sri Lanka's first saint, the 17th Century missionary Joseph Vaz, with huge crowds expected to attend.
People began lining up on Tuesday to secure a place, reports from the Sri Lankan capital say.
Later Pope Francis will speak at prayers in Madhu in the north - a region which saw some of the fiercest fighting of the 26-year war.
The conflict, arising from ethnic tensions between the majority Sinhalese and the Tamil minority, ended in 2009 when the army defeated separatist Tamil rebels. The United Nations said both sides committed atrocities against civilians.
The government consistently denied allegations that it was responsible for the deaths of many thousands of civilians in the final phase of that war. Last year the UN approved an inquiry into alleged war crimes.
Just over 7% of Sri Lanka's population are Christian, mostly Catholic - but they include both Sinhalese and Tamils. About 70% of Sri Lankans are Buddhist, with 13% Hindus and 10% Muslims.
The last papal visit was 20 years ago, when Pope John Paul II was boycotted by Buddhist leaders. But on Tuesday, Pope Francis met a group of Buddhist, Hindu and Muslim leaders, urging reconciliation.
"For the sake of peace, religious belief must never be allowed to be abused in the cause of violence and war," he said.
"We must be clear and unequivocal in challenging our communities to live fully the tenets of peace and coexistence found in each religion, and to denounce acts of violence when they are committed."
His visit comes amid change in Sri Lanka, where Maithripala Sirisena took office as president on Friday, replacing Mahinda Rajapaksa.
Critics said Mr Rajapaksa's leadership had been marred by increasing corruption and authoritarianism.
There have been early signs of reform under the new leader, but it is not yet clear if his approach to addressing the legacy of the war will differ from his predecessor, who is seen as a hero by many Sri Lankans for ending the conflict.
(BBC News)
