He was accompanied by his cabinet ministers Harjit Sajjan, Navdeep Bains, Bardish Chagger, Kirsty Duncan, and Amarjeet Sohi.
The Canadian prime minister was escorted by Mallika Ahluwalia, the CEO and Curator of the museum, Union minister Hardeep Singh Puri, Minister of Local Government, Culture and Tourism Navjot Singh Sidhu, and Member of Parliament Gurjeet Singh Aujla.
Trudeau spent nearly 25 minutes at the museum.
He spent some time in the gallery of migration, hearing stories and looking at objects carried by people as they fled their homes and moved across the newly-drawn borders at the time of Independence.
The Canadian premier paused for a while at the well in the Gallery of Divisions, dedicated to the women who were lost at the time of partition.
He spent the maximum time in the Gallery of Hope, which focuses on love and reconciliation. He left a note on the Tree of Hope writing that the museum is "a poignant reminder that dividing people is never the answer; we must learn to live together and love our differences."
Curator Ahluwalia said: "We are very grateful to Prime Minister Trudeau for visiting the Partition Museum. As Canada has a vibrant Punjabi community, the museum is very keen to record and include the stories of Punjabis settled there."
Trudeau also shared his thoughts on the Partition Museum, saying "to think of the lives torn apart, the violence and loss... We need to remember that it's always easy to divide people. It's much more difficult but it's the only path to bring people together in love and understanding. We have to be ever vigilant that that is what we are putting into the world and that is the way we are building our future."
The Canadian prime minister is in India on a week-long visit. Earlier in the day, he paid obeisance at the Golden Temple in Amritsar.
The Partition Museum is the world's first museum dedicated to the partition of the Indian sub-continent in 1947. The museum is dedicated to all those millions impacted in the largest migration in human history and is a space of reconciliation.
The museum uses multi-media exhibits including oral histories, archival footage, historical newspapers, official files, as well as personal documents and objects carried by individuals and families who lived through the Partition to tell the story.
It also aims to become a comprehensive archive on the Partition. The museum opened with a curtain raiser exhibition in Octobber 2016 and opened all its galleries to the public on August 17, 2017.