The name Tondo can be derived from its Old Tagalog name, Tundun as inscribed in the Laguna Copperplate Inscription of 900 AD, the earliest native document found within the Philippines.

Dutch anthropologist Antoon Postma, the first to translate the copperplate, believes the term tundun originated from Sanskrit,[3] which was used alongside Malay as a language of politics and religion in the area at the time.

[4] On the other hand, French linguist Jean-Paul Potet, supposed that the Aegiceras corniculatum, which at the time was called "tundok" ("tinduk-tindukan" today), was the most likely origin of the name.

In the 1970s, the World Bank provided funds to improve conditions in Tondo which led the increase of rent prices and a property boom in the area.

The slums that were upgraded were legalized but these areas remain vastly different from other parts of Manila with higher population density, more irregular road and plot patterns, and uncontrolled housing.

[12] The area also hosted Smokey Mountain, a landfill which served Metro Manila and employed thousands of people from around the 1960s until its closure in the late 1990s.

[13] Urbanization as well as the Lina Law which favors squatting over land owners has resulted in Tondo being one of the most densely populated areas in the world at 69,000 inhabitants per square kilometer (180,000/sq mi).

In October 2024, Mayor Honey Lacuna and Felma Carlos-Tria led the time capsule lowering and groundbreaking of Universidad de Manilas's 10-storey school building in a 1,500-square-meter lot at Vitas Skate Park.