The new find appears to be from the same species, researchers said.
A team co-led by Eudald Carbonell, director of the Catalan Institute of Human Paleo-Ecology and Social Evolution, reported its find in today's issue of the scientific journal Nature.
The timing of the earliest occupation of Europe by humans that emerged from Africa has been controversial for many years.
Some archeologists believe the process was a stop-and-go one in which species of hominins - a group that includes the extinct relatives of modern humans - emerged and died out quickly only to be replaced by others, making for a very slow spread across the continent, Carbonell said.
Until now, the oldest hominin fossils found in Europe were the Homo antecessor ones, also found at Atapuerca, but at a separate site, and Ceprano, Italy.
Carbonell's team has tentatively classified the new fossil as representing an earlier example of Homo antecessor. And, critically, the team says the new one also bears similarities to much-older fossils dug up since 1983 in the Caucasus at a place called Dmanisi, in the former Soviet republic of Georgia. These were dated as being up to 1.8 million years old.
Carbonell believes hominins, which emerged from Africa and settled in the Caucasus, eventually evolved into Homo antecessor, and that the latter populated Europe not 800,000 years ago, but at least 1.3 million years ago.