The aerospace industry ranks among the largest manufacturing industries in the world facing a significant growing phase as well as an increased competition. This paper addresses the scheduling of a set of jobs in a paced assembly line in presence of uncertainty affecting the availability of production resources, stemming from the assembly process in the aircraft manufacturing industry. The production problem is modeled as a no-wait paced permutation flow shop and solved providing a robust scheduling solution minimizing the conditional value-at-risk (CVaR) of the residual work content, i.e., the amount of workload that cannot be completed during the cycle time in the stations, due to a lack of available resources. A branch-and-bound approach is developed and applied to randomly generated instances as well as to an industrial problem related to the production of aircrafts. © 2019 Elsevier Ltd