Conjugated polymers are promising actuation materials for bio- and micromanipulation systems, biomimetic robots, and biomedical devices. Sophisticated electrochemomechanical dynamics in these materials, however, poses significant challenges in ensuring their consistent, robust performance in applications. In this paper, an effective adaptive control strategy is proposed for conjugated polymer actuators. A self-tuning regulator is designed based on a simple actuator model, which is obtained through reduction of an infinite-dimensional physical model and captures the essential actuation dynamics. The control scheme is made robust against unmodeled dynamics and measurement noises with parameter projection, which forces the parameter estimates to stay within physically meaningful regions. The robust adaptive control method is applied to a trilayer polypyrrole (PPy) actuator that demonstrates significant time-varying actuation behavior in air due to the solvent evaporation. Experimental results show that, during 4-h continuous operation, the proposed scheme delivers consistent tracking performance with the normalized tracking error decreasing from 11% to 7%, while the error increases from 7% to 28% and to 50% under a proportional-integral-derivative (PID) controller and a fixed model-following controller, respectively. In the meantime, the control effort under the robust adaptive control scheme is much less than that under PID, which is important for prolonging the lifetime of the actuator.