Van Maanen, who was born at Sneek in the Netherlands, studied at the University of Utrecht, where he obtained his doctorate in 1911. He worked at the University of Groningen from 1909 to 1911 when he moved to America. After working briefly at the Yerkes Observatory he took up an appointment in 1912 at the Mount Wilson Observatory in California, where he remained for the rest of his career.

Van Maanen specialized in measuring the minute changes in position of astronomical objects over a period of time, from which he could determine their proper motion and parallax. These objects included stars, clusters of stars, and nebulae. Between 1916 and 1923 he produced a number of measurements of spiral nebulae from which he calculated their rotation rate. This was at the time of the controversy between astronomers as to whether such nebulae were island universes in their own right or part of our own Galaxy. Van Maanen's results were therefore of considerable significance, for whether one can detect rotation in a distant body and measure its rate of rotation partly depend on the distance of the object from the observer. The rotation of about 0.02 seconds of arc per year that he obtained from a number of nebulae over a period of seven years seemed to be indisputable evidence against the emerging view that such objects as the Andromeda nebula were really separate remote star systems. This was certainly the view that Harlow Shapley took in 1920 as he could see no reason to doubt the work of van Maanen, his close friend, who was known to be a careful and competent observer.

Van Maanen's work was, however, incompatible with the growing body of measurements produced by Edwin Hubble, also at Mount Wilson. These suggested that nebulae like Andromeda were as much as 800,000 light-years away, at which distance it was inconceivable that any internal motion should be detectable. As no one, including van Maanen himself, had any idea where he had gone wrong, his work became something of a curiosity and tended to be ignored. Other astronomers, like Knut Lundmark in 1923, failed to reproduce his results while in 1935 van Maanen was able to detect a displacement only about half that found in the 1920s. When in the same year Hubble also reported failure to detect the rotation, it became widely accepted that there was some unknown instrumental or personal error in van Maanen's work.

It is unlikely to have been an instrumental error as Hubble used the same instruments while a later computer analysis of his work has revealed no major computational errors. This only leaves unconscious personal error and recent work has shown that a systematic error of only 0.002 millimeter in the measurements of points on photographic plates would be sufficient to produce his results. The same systematic error also occurred in his work on the strength of the solar magnetic field, which he considerably overestimated.

He did however discover the second white dwarf, since named van Maanen's star, with a density some 400,000 times that of the Sun.