Howden Junior School in East Yorkshire removed the house names Drake, Nelson and Raleigh over the summer after reconsideration in the wake of the Black Lives Matter movement's resurgence.
Headteacher Lee Hill said he had received a "passionate and, quite frankly, brave" email from a former pupil pointing out the historical figures' links to racism, slavery and oppression.
In a lengthy and open post on the school's Facebook page, Mr Hill wrote that the email "set off a chain of events and reflection" over the house names, which were tributes to Francis Drake, Lord Nelson and Sir Walter Raleigh - the first of which was known to be a slave trader.
"Beyond the fact they have been in places for decades, we had no tangible reason behind them," the post said.
"We didn't teach them in our curriculum. We clearly didn't know all aspects of their history. None of our pupils knew who they were (beyond sailors), nor did they feel like they could relate to them.
"And, more importantly, a member of our community strongly (and understandably) was affected by their association with the school in a negative way."
The junior school has now unveiled new names for its three houses as well as a newly-created one, while saying the colours attributed to each house would remain.
Its houses have now been renamed Thunberg, Gorman, Malala and Rashford in nods to climate change activist Greta Thunberg, American poet laureate Amanda Gorman, girls' education campaigner Malala Yousafzai and footballer Marcus Rashford.
Mr Hill said the new names were pitched by the school council and better represented both the local and wider international community.
The school has also commissioned local artist, Amy Smith, to create portraits of the new figures heading its four houses which are to be displayed in the school.
Mr Hill added: "This is a change driven by the children of our school in its truest sense - something we should all be incredibly proud of. The manner in which they have made this change is incredible."
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