The low resolution spectropolarimetric observations obtained with FORS1 at the VLT have often been used for investigating magnetic fields in hot stars. Here we describe the first investigation of the magnetic field over the stellar rotation in a cool late-type star, FK Com, based on FORS1 spectropolarimetry. We measure the mean longitudinal magnetic field from nine circularly polarised spectra, and study its behaviour over the stellar rotation. The magnetic field measurements are compared to a simultaneous stellar surface temperature map obtained with Doppler imaging techniques. These observations reveal two cool spots on the surface, and indicate that the main cool region coincides with the maximum value of the mean longitudinal magnetic field. Additionally, only 0.25 in phase apart from the main spot, the secondary spot is located at a similar phase to the field minimum. The observations can be interpreted as two spots having different magnetic field polarities, implying that the starspot configuration on FK Com is similar to that observed in the Sun.