While Thutmose was the son of a nonroyal mother, he may have strengthened his claim to the throne by marrying Ahmose, perhaps a relative of his predecessor, probably some time before his accession. He also possibly was associated with his predecessor as coregent for an unspecified period, as is attested by a chapel found at Thebes. On his accession day, he communicated his new titulary and coronation in a letter to the viceroy of Nubia.

In his second year Thutmose led a riverborne expedition deep into Nubia, beyond his predecessor's frontier. As shown by inscriptions carved along the way, he thrust past the Fourth Nile (Nile River) Cataract and set up a new boundary at Kurgus. The venture is attested by the biographies of two Upper Egyptians who were among the forces that made the campaign. One reason for the deep thrust into Nubia was the land's rich gold deposits, which were intensely exploited during the 18th dynasty (1539–1292 BCE). Another motivation was the fact that a hostile Kushite kingdom, centred near the Third Cataract, had seriously menaced Egypt during the 17th dynasty (c. 1630–1540 BCE; see ancient Egypt: The Second Intermediate period (Egypt, ancient)).

After his Nubian war Thutmose penetrated to the Euphrates River in the vicinity of Carchemish in Syria as he continued the pursuit of the Hyksos, Asiatic rulers who had recently dominated Egypt. One of the texts from Nubia states that already before the Syrian foray, Thutmose claimed the Euphrates as his border. Although no evidence of earlier campaigns survives, the Nubian text implies that deep penetration of Syria had already occurred.

Within Egypt, Thutmose thoroughly renovated the Middle Kingdom (Egypt, ancient) (1938–c. 1630 BCE) temple of Amon at Thebes. He erected an enclosure wall and two pylons at the western end, with a small pillared hall in between. Two obelisks were added in front of the outer pylon. Thutmose created the axial temple, which became standard for the New Kingdom (Egypt, ancient) (1539–1075 BCE).

Two crown princes predeceased the king. One had become commander of the armies and was assigned to Memphis, near present-day Cairo, which in the New Kingdom became a military operations centre. Thutmose set the example for later kings, who likewise assigned their crown princes to Memphis, where they were schooled in the military arts.

Thutmose also was the first king to cut his tomb in the Valley of the Kings (Kings, Valley of the) at Thebes, probably to obtain greater security for it. It was he who expanded the cemetery workers' village at Dayr al-Madīnah, in western Thebes, and who completed the organization of the necropolis staff begun by his predecessor. The length of Thutmose's reign is still uncertain, and his highest attested date is year nine.