A biomagnetic measurement method, a biomagnetic measuring device, and a biomagnetic measuring system. The method and the biomagnetic measuring device includes obtaining first measurement data output from a magnetic field detector upon giving a stimulus to a subject in a first state where a site of interest of the subject is made close to the magnetic field detector, and obtaining second measurement data output from the magnetic field detector upon giving a stimulus to the subject in a second state where a site to which the stimulus is given and a position of the site to which the stimulus is given are equivalent to a site to which the stimulus is given and a position of the site to which the stimulus is given in the first state, respectively, and the site of interest of the subject is separated from the magnetic field detector with reference to the first state.