Conjugated polymers are promising actuation materials for bio and micromanipulation systems, biomimeticrobots, and biomedical devices. Sophisticated electrochemomechanical dynamics in these materials, however,poses significant challenges in ensuring their consistent, robust performance in applications. In this paper aneffective adaptive control strategy is proposed for conjugated polymer actuators. A self-tuning regulator isdesigned based on a simple actuator model, which is obtained through reduction of an infinite-dimensionalphysical model and captures the essential actuation dynamics. The control scheme is made robust againstunmodeled dynamics and measurement noises with parameter projection, which forces the parameter estimates tostay within physically-meaningful regions. The robust adaptive control method is applied to a trilayer polypyrroleactuator that demonstrates significant time-varying actuation behavior in air due to the solvent evaporation.Experimental results show that, during four-hour continuous operation, the proposed scheme delivers consistenttracking performance with the normalized tracking error decreasing from 11% to 7%, while the error increasesfrom 7% to 28% and to 50% under a PID controller and a fixed model-following controller, respectively. In themean time the control effort under the robust adaptive control scheme is much less than that under PID, whichis important for prolonging the lifetime of the actuator.