Scheduling is key towards improving the performance of a Flexible Assembly Line (FAL). In this paper, a Bilevel Differential Evolution (BiDE) algorithm to solve a FAL scheduling problem is proposed. The BiDE algorithm optimizes the performance of the FAL with respect to two criteria: the weighted sum of Earliness/Tardiness (E/T) penalties and the balance of the FAL. The performance of BiDE is evaluated using the data sets available in the literature and an evolutionary heuristic algorithm published earlier called BiGA. The experimental results show that the BiDE algorithm can solve the FAL scheduling problem effectively and exhibits a superior performance over BiGA. © 2004-2012 IEEE.