This fluorescence microscope system (200) is provided with an excitation unit (10) which outputs a line illumination (Ex) for excitation of a fluorescent sample (S), an observation optical system (40) which focuses the line illumination (Ex) outputted by the excitation unit (10) and also extracts fluorescence from the fluorescent sample (S), and a control unit (8) which controls the focus position (Z) of the observation optical system (40) on the basis of the evaluation value of the fluorescence extracted by the observation optical system (40). Control of the control unit (80) includes: thinning adjustment in which the focus position (Z) of the observation optical system (40) is moved at a prescribed thinning interval and a first focus position (Z1) is determined where the evaluation value satisfies a prescribed condition; and microadjustment in which the focus position of the observation optical system (40) is moved within a movement range narrower than the range of movement during the thinning adjustment on the basis of the first focus position (Z1) determined by the thinning adjustment.