Born in Jackson, California, Aitken obtained his AB in 1887 and his AM in 1892 from Williams College, Massachusetts. He began his career at the University of the Pacific, then in San Jose, as professor of mathematics from 1891 until 1895 when he joined the staff of Lick Observatory, Mount Hamilton, California. He remained at Lick for his entire career, serving as its director from 1930 until his retirement in 1935.

Aitken did much to advance knowledge of binary stars, i.e. pairs of stars orbiting about the same point under their mutual gravitational attraction. He described over 3000 binary systems and published in 1932 the comprehensive work New General Catalogue of Double Stars Within 120° of the North Pole. He also produced the standard work The Binary Stars (1918).