This paper presents the design of a flight control system (FCS) for the lateral axis of a very flexible High Altitude Long Endurance (HALE) aircraft. To ensure that the HALE aircraft stays within its defined flight envelope, the FCS design incorporates roll attitude tracking requirements in the form of a coordinated turn and disturbance rejection requirements in the form of adequate discrete gust and continuous turbulence mitigation. The HALE aircraft itself is prone to aeroelastic effects. The paper shows via an aeroelastic load analysis, that a FCS not explicitly considering loads in its design is insufficient, as peak loads in the fuselage torsion and vertical tail bending moment are increased. As a response to these findings, a design approach for lateral FCS is proposed, which allows to weight the structural loads at the vertical tail root against the maximum roll attitude during the gust encounter. The benefit of this control design may result either in a potential decrease in structural weight or strength margins of the fuselage. Finally, the resulting lateral axis FCS design is validated in non-linear simulations of lateral gust encounters and the reduction of maximum loads on the vertical tail during worst case gusts is shown.