An image pickup system comprising: an image pickup device in which a plurality of pixels for performing photoelectric conversion are arrayed in a two-dimensional shape in units of horizontal lines; an image pickup control unit configured to set a predetermined exposure period to be longer than a period required for readout of all horizontal lines and cause the image pickup device to sequentially start exposure of the image pickup device for each of the horizontal lines of a frame, and, after causing the image pickup device to start exposure of a last horizontal line of said frame, cause the image pickup device to sequentially perform readout for each of the horizontal lines on which the predetermined exposure period elapses from the exposure start to thereby perform control such that an all line exposure period (Ta) in which all the horizontal lines are simultaneously exposed and a non-all line exposure period (Tr) in which at least one of the horizontal lines is exposed but which is not the all line exposure period (Ta) are generated, the non-all line exposure period (Tr) directly following the all line exposure period (Ta); a light source configured to emit illumination light emitted to an object which is a target of image pickup by the image pickup device; a light source driving unit configured to drive the light source to be capable of adjusting a light amount of the illumination light; and a light adjustment controlling unit configured to control the light source driving unit, in a first light adjustment mode in which a light amount of the illumination light is not zero during a second period, while maintaining a light amount of the illumination light in a first period at a predetermined level, such that the light amount of the illumination light during the second period is made different from a light amount of the illumination light in an immediately preceding second period of an immediately preceding frame, wherein the first period is a period in the all line exposure period (Ta), and the second period is a period including the all line exposure period (Ta) other than the first period and the non-all line exposure period (Tr). an image pickup device in which a plurality of pixels for performing photoelectric conversion are arrayed in a two-dimensional shape in units of horizontal lines; an image pickup control unit configured to set a predetermined exposure period to be longer than a period required for readout of all horizontal lines and cause the image pickup device to sequentially start exposure of the image pickup device for each of the horizontal lines of a frame, and, after causing the image pickup device to start exposure of a last horizontal line of said frame, cause the image pickup device to sequentially perform readout for each of the horizontal lines on which the predetermined exposure period elapses from the exposure start to thereby perform control such that an all line exposure period (Ta) in which all the horizontal lines are simultaneously exposed and a non-all line exposure period (Tr) in which at least one of the horizontal lines is exposed but which is not the all line exposure period (Ta) are generated, the non-all line exposure period (Tr) directly following the all line exposure period (Ta); a light source configured to emit illumination light emitted to an object which is a target of image pickup by the image pickup device; a light source driving unit configured to drive the light source to be capable of adjusting a light amount of the illumination light; and a light adjustment controlling unit configured to control the light source driving unit, in a first light adjustment mode in which a light amount of the illumination light is not zero during a second period, while maintaining a light amount of the illumination light in a first period at a predetermined level, such that the light amount of the illumination light during the second period is made different from a light amount of the illumination light in an immediately preceding second period of an immediately preceding frame, wherein the first period is a period in the all line exposure period (Ta), and the second period is a period including the all line exposure period (Ta) other than the first period and the non-all line exposure period (Tr).