The nine-year-old died from "severe respiratory difficulties" at the Barranquilla hospital, facility representative Guiomar Martinez told reporters yesterday.
A five-year-old is still hospitalized in "critical but stable" condition, Martinez added.
The May 18 incident shocked the nation after the children burned to death when an overcrowded bus burst into flames and the driver fled the scene, pursued by a mob that stoned his house.
A total of 31 died on the spot, with the two other deaths taking place while the children were hospitalized. Colombia decreed three days of national mourning after the tragedy.
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The pastor and the 56-year-old driver are in pre-trial detention and face a maximum sentence of 60 years behind bars.
The children, aged between three and 12 years old, were returning from evangelical church services in the small northern town of Fundacion. The driver lost two of his own children in the tragedy.
Two dozen other children were also initially hospitalized, most of them with second- or third-degree burns.