Hominins first arrived in the Philippines during a period of lower global sea levels between 1 million years ago (1 mya) to 700,000 years ago (700 kya). Early migrations to its largest island Luzon happened in the Pleistocene and most likely began from the south in Borneo, an island once connected to mainland Asia. From there, hominins crossed narrow sea barriers and reached Luzon by passing through Palawan then Mindoro. The oldest known hominin fossils belong to the extinct Homo luzonensis, which inhabited present-day Cagayan Valley around 67 kya. The species was characterized by its short stature and relatively small brain.

The Philippines' early inhabitants were hunter-gatherers. Apart from wild pigs, deer, and bovines, they hunted a diverse range of large animals like rhinoceros, giant turtles, and elephants. The tools they manufactured were made of stone and were simple, irregularly shaped, convenient, and disposable. Dark-skinned, short-statured, and frizzy-haired peoples called Aytas or Negritos reached the archipelago by about 50–40 kya and were the first anatomically modern humans to do so.

The current demarcation between this period and the early history of the Philippines is April 21, 900, which is the equivalent on the Proleptic Gregorian calendar for the date indicated on the Laguna Copperplate Inscription—the earliest known surviving written record to come from the Philippines. This period saw the immense change that took hold of the archipelago from Stone Age cultures in 50000 BC to the emergence of coastal trading centers in the fourth century, continuing on with the gradual widening of trade until 900 and the first surviving written records.

The Philippines is an archipelago that lies in the Earth's tropics, giving it a warm climate and making it prone to severe rainfall. Physical, chemical, and biological processes in humid environments – such as thermal decomposition, weathering, erosion, and bioturbation – make organic matter and sediments hard to preserve and easy to destroy. Finding samples that would otherwise be useful in constructing a detailed archaeological record is therefore difficult. For example, there is currently a scarce amount of bones discovered in archaeological sites across the country.

Early hominin species first populated the Philippines by crossing the surrounding waters during the Last Glacial Period, when sea levels were lower and present-day islands were easier to reach due to land bridges and narrower straits. These migrations began in the Chibanian or Middle Pleistocene age, between 1 million to 700 thousand years before present (YBP). It was possible for hominins to reach a new island purely by accident.

There is currently no material evidence that hominins built watercraft capable of navigating the Philippine seas. Regardless, they must have found a way to drift or raft across vast expanses of water, with floating vegetation as proposed objects for doing so. Archaeologist Thomas Ingicco suggested that mangroves uprooted by disasters like typhoons could serve as such natural rafts.

To reach the Philippines during the Pleistocene, hominins had to come from either the north in Taiwan or the south in Borneo. Borneo was the most likely starting point. It was fairly close to the Philippines and, due to low sea levels, was connected to mainland Asia through the Sundaland landmass. Hominins from Borneo would have reached Luzon by passing through Palawan first, followed by Mindoro; they may have also entered the Philippines via the Sulu Archipelago.

Sulawesi, an Indonesian island to the south, was also a likely starting point for hominin migration. Hominins coming from Sulawesi would have arrived at the Philippines via Mindanao. Although possible, the least likely migration scenario is a sea crossing from Taiwan to Luzon via the Luzon Strait. The ocean currents were highly turbulent and required advanced navigation technologies to overcome.