Most of the research effort in the field of HAP communications until now has been invested in the physical layer of the protocol stack, and in the radio related issues in particular. However, the overall system throughput is limited by the performance of the transport layer. Since HAPs will be used in networks with different topological complexity, various kinds of wireless communications links, bit error rates, and various mixtures of multimedia traffic, the control flow in such networks may present itself as a non-linear and stochastic process. Therefore we introduced a fuzzy control of the throughput in the TCP. Our approach is based on the off-line synthesis of the Takagi-Sugeno fuzzy controller based on the simulation data and on-line flow control by the synthesized controller that is built in the conventional TCP. In the paper we present the ns2-based simulation results.