Reaction wheels (RW), the most common attitude control systems in satellites, are highly prone to failure. A satellite needs to be oriented in a particular direction to maneuver and accomplish its mission goals; losing the reaction wheel can lead to a complete or partial mission failure. Therefore, estimating the remaining useful life (RUL) over long and short spans can be extremely valuable. The short-period prediction allows the satellite’s operator to manage and prioritize mission tasks based on the RUL and increases the chances of a total mission failure becoming a partial one. Studies show that lack of proper bearing lubrication and uneven frictional torque distribution, which lead to variation in motor torque, are the leading causes of failure in RWs. Hence, this study aims to develop a three-step prognostic method for long-term RUL estimation of RWs based on the remaining lubricant for the bearing unit and a potential fault in the supplementary lubrication system. In the first step of this method, the temperature of the lubricants is estimated as the non-measurable state of the system using a proposed adjusted particle filter (APF) with angular velocity and motor current of RW as the available measurements. In the second step, the estimated lubricant’s temperature and amount of injected lubrication in the bearing, along with the lubrication degradation model, are fed to a two-step particle filter (PF) for online model parameter estimation. In the last step, the performance of the proposed prognostics method is evaluated by predicting the RW’s RUL under two fault scenarios, including excessive loss of lubrication and insufficient injection of lubrication. The results show promising performance for the proposed scheme, with accuracy in estimation of the degradation model’s parameters around 2–3% of root mean squared percentage error (RMSPE) and prediction of RUL around 0.1–4% error.