The invention relates to an image pickup apparatus, an image pickup system and control method thereof. An image pickup apparatus includes a detection unit in which a matrix of pixels converts radiation or light into analog electrical signals, a reading circuit configured to perform signal processing operation by reading the analog electric signals on a row-by-row basis, an A/D converter configured to convert a pixel signal output from the reading circuit into pixel data, and a correction processing unit configured to correct the pixel data. A control unit performs control processing so that the reading circuit outputs reset signals to the A/D converter in a period in which the signal processing operation of a predetermined row is performed, the A/D converter converts the reset signals into pieces of reset data in the period, and the correction processing unit averages the pieces of reset data output from the A/D converter and performs subtraction with the averaged reset data and the pixel data output from the A/D converter.