The pontiff addressed around 65,000 people in the capital Sarajevo as part of a one-day visit.
He also released doves outside of Bosnia's presidential building, to symbolise peace and unity.
His calls for reconciliation refer to the Bosnian civil war between 1992 and 1995, where 100,000 people died, at least 20,000 women were raped and approximately two million made homeless - making it the worst conflict since World War II.
Three main ethno-religious groups made up the conflict: Muslim Bosniaks, Orthodox Serbs and Catholic Croats. The United Nations has resolved that the Serbs committed genocide against the Bosniaks in the conflict.
This is reflected in the casualty numbers, where according to the Research and Documentation Center in Sarajevo more than 62,000 Bosniaks died, compared to more than 24,000 Serbs and over 8000 Croats.
Pope Francis told crowds: "War never again! War means children, women and the elderly in refugee camps; it means forced displacement, destroyed houses, streets and factories. Above all countless shattered lives."
Prior to arriving in Sarajevo, he said it was "... a city that has suffered so much in history. But now it is walking along the path to peace.
"I'm making this trip as a sign of peace, and as a prayer for peace."