In the paper, a new scheduling strategy for assembly systems consisting of cooperating Automated Guided Vehicles (AGVs) based on their remaining operational time is developed. The operational time is associated with state of charge and state of health of the AGV battery. While the latter is defined as a possible number of repetitions of a set of given tasks, both are impossible to measure on-line directly with conventional sensors. Therefore, a novel state-of-charge estimator is proposed, which uses battery current and voltage sensor readings. In contrast to the approaches presented in the literature, a comprehensive analysis of its convergence is provided. Subsequently, a state-of-health predictor is developed. With the above measures, a new control strategy for cooperative AGVs is proposed. It is achieved by the allocation of alternative tasks among two cooperating robots referring to the state of the accomplished tasks from the previous stage of the assembly process. The proposed method allows a predictive control of assembly processes with several constraints, e.g., productivity of each assembly station, speed of the communication, or operation capability of the robots involved in the assembling process. The final part of the paper shows an experimental study exhibiting the performance of the proposed approach.