Provided are an imaging apparatus capable of preventing deterioration in quality of a captured image to be captured in a case where imaging is performed by using the driving according to the global shutter method and the driving according to the rolling shutter method in combination, an operation method thereof, and an operation program thereof. The digital camera includes an imaging element 5 that has a plurality of pixels 61 each including a photoelectric conversion element 61A and a charge holding section 61B, and a driving controller 11A that performs driving control of the imaging element 5 according to a global shutter method while continuously performing driving control of the imaging element 5 according to a rolling shutter method. The driving controller 11A makes a first time, which is necessary for reading a signal obtained from one of pixel rows 62 under the driving control according to the rolling shutter method, longer than a second time which is necessary for reading the signal obtained from one of the pixel rows 62 under the driving control according to the global shutter method.