An apparatus for estimating a communication response time between different controllers of a vehicle may include: a data transmitter of a first controller configured to measure an actual message response time required until a response message is received from a second controller after the first controller transmits a message to the second controller; an estimator of the first controller configured to receive a size of the message from the data transmitter of the first controller and reflect the received size to estimate the actual message response time according to a designated estimation logic; and a result data processor of the first controller configured to correct an estimation parameter used when the estimator estimates the message response time based on a difference between the actual message response time and the estimated message response time acquired through the estimator, and update the existing estimation parameter of the estimator.