Disclosed is an apparatus and method for estimating a channel capacity of an end-to-end terminal. The channel capacity estimating method of the end-to-end terminal includes calculating an average value of channel capacities for each size of data packets, the data packets varying in size, measuring an actual channel capacity with respect to the data packets, and deriving a linear model of a channel capacity based on the size of the data packets using the average value of the channel capacities and the actual channel capacity.