Autonomous systems are highly complex and present unique challenges for the application of formal methods. Autonomous systems act without human intervention, and are often embedded in a robotic system, so that they can interact with the real world. As such, they exhibit the properties of safety-critical, cyber-physical, hybrid, and real-time systems. This EPTCS volume contains the proceedings for the third workshop on Formal Methods for Autonomous Systems (FMAS 2021), which was held virtually on the 21st and 22nd of October 2021. Like the previous workshop, FMAS 2021 was an online, stand-alone event, as an adaptation to the ongoing COVID-19 restrictions. Despite the challenges this brought, we were determined to build on the success of the previous two FMAS workshops. The goal of FMAS is to bring together leading researchers who are tackling the unique challenges of autonomous systems using formal methods, to present recent and ongoing work. We are interested in the use of formal methods to specify, model, or verify autonomous and/or robotic systems; in whole or in part. We are also interested in successful industrial applications and potential future directions for this emerging application of formal methods.