An image pickup system capable of obtaining images to be observed without giving a sense of discomfort to an observer, while moving as fast as possible. The image pickup system comprises an image pickup device, and a drive section arranged to rotate the image pickup device in a first direction and a second direction orthogonal to the first direction, respectively. A directive is issued on a rotation target angle of the image pickup device associated with the first direction and a rotation target angle of the image pickup device associated with the second direction. A component higher than a specified cut-off frequency in a command signal associated with the first direction entered from the command section is cut. A component higher than a specified cut-off frequency in a command signal associated with the second direction entered from the command section is cut. A rotation drive command associated with the first direction and a rotation drive command associated with the second direction are outputted to the drive section, respectively, based on each output of the first signal processing section and the second signal processing section. The specified cut-off frequency of the first signal processing section is lower than that of the second signal processing section.