Palaeoloxodon falconeri derives from the 4 metre tall straight-tusked elephant (P. antiquus), which arrived in Europe approximately 800,000 years ago. The oldest radiometrically dated fossils of Palaeoloxodon on Sicily date to around 500,000 years ago.
The chronology of the species compared to that of the larger endemic species of Palaeoloxodon on Malta and Sicily, the  tall Palaeoloxodon mnaidriensis, is somewhat uncertain. It is generally thought that P. falconeri is the earlier species dating to the Middle Pleistocene, and that P. mnaidriensis descends from a subsequent separate late Middle Pleistocene colonisation of the island by P. antiquus, suggested to date to approximately 200,000 years ago.