Tomitaro Makino was born in Sakawa, Kōchi to a prestigious sake brewer. His parents died during his early childhood, and he was raised mainly by his grandmother. Though he dropped out of school after two years, he cultivated a strong interest in English, geography, and especially in botany. In 1880, he became a teacher at the primary school in his hometown, where he published his first academic botanical paper.
In 1884, he moved to Tokyo to pursue his botanical interests at the University of Tokyo where he worked with
Ryokichi Yatabe. He married in 1890 and would later have 13 children.