The invention provides a detection system and method of signal transmission delay for fan chip. The detection system comprises a circuit board, a fan chip and a control unit. The control unit generates a first pulse signal having a specific pulse pattern, and send the first pulse signal to the fan chip. When the fan chip is operating in a detection mode of signal transmission delay according to the first pulse signal, the fan chip copies the specific pulse pattern of the first pulse signal to generate a second pulse signal having the specific pulse pattern, and send the second pulse signal to the control unit. The control unit calculates a time difference between a time that sends the first pulse signal and a time that receives the second pulse signal, so as to obtain a delay time of signal transmission between the control unit and the fan chip.