Kuiper became a friend of the Ehrenfest family in his role as tutor to the physicist's son.

Kuiper, Bok, and fellow student Piet Oosterhoff pursued their studies in astronomy together, learning from Willem de Sitter, Jan Woltjer, and Jan Oort, in addition to those named above. In his student years, Kuiper joined the Dutch solar eclipse expedition to Sumatra for eight months in 1929. He learned Malay and wandered among the native villages painting beach scenes and studying the local customs. Then, on the eve of the eclipse he discovered that another astronomer had incorrectly oriented the spectrograph slit on one of the cameras; the correction was made just in time to secure important data during the eclipse the next day.

In 1929, Kuiper began correspondence with the great double-star astronomer Robert Grant Aitken, at Lick Observatory of the University of California, and submitted his earliest measurements for criticism. He also outlined for Aitken the essence of the statistical study which was to occupy him for over a decade. Kuiper did his doctoral thesis on binary stars with Hertzsprung, and he received his Ph.D. on completion of this work in 1933. That same year he traveled to the United States to become a Kellogg Fellow (and then a Morrison Fellow) at Lick Observatory near San Jose on Mount Hamilton.

Under Aitken's tutelage, Kuiper continued his work on binary stars at Lick, where he systematically examined stars of large parallax for duplicity. He had delayed publication of his thesis until he could improve the observational data for double stars with large differences in brightness between the components. Observing visual doubles with the 12- and 36-inch refractors and making color-index measurements with the Crossley 36-inch reflector, he discovered numerous binaries and many white dwarf stars.