This paper describes the design and implementation of a three-axis acceleration control autopilot for an asymmetric tail-controlled, skid-to-turn tactical missile. In an earlier flight test, degraded autopilot performance was attributed to multiple disturbances and uncertainties and the presence of hidden coupling terms, giving rise to a miss distance of greater than 20 m. To address these issues, the missile dynamics are decomposed into the angular rate dynamics as fast and the acceleration dynamics as slow subsystem using the singular perturbation theory to analyze a multi-time-scale property. Multifrequency extended state observers are then incorporated into the gain scheduling technique to attenuate disturbances, thus enhancing the control performance significantly. In the proposed engineering/practical design framework for missile autopilot, simple, conventional, and explicit tuning rules are provided. And the proposed control scheme can achieve input-to-state stability across the entire flight envelope under unknown but bounded disturbances. The advantages of the method over existing benchmark approaches are shown through nonlinear numerical simulations. This is supported by evidence from a new flight test result with a miss distance of only 2 m.