In this paper, reliability of missile system in its total life cycle is evaluated in terms of its subsystems’ reliability, using Continuous Time Markov Chains (CTMC) and Monte Carlo simulation method, finally results of both methods are compared. Missile system’s life cycle includes storage, pre-launch and operation states. Missile system is composed of variety of components and materials, hence different environmental conditions and various stresses imposed on missile system in each state during its life cycle, stimulates diverse failure modes and mechanisms. Therefore, failure probability distribution function differs for each subsystem in each state. Flight control, mechanical parts and equipment, engine and warhead are four main subsystems of the missile system. They are linked in series therefore each one’s failure will result in system’s failure. Exponential, Weibull, Lognormal and Gompertz distributions are used for subsystems’ modeling in different life cycle states. Unlike many other researches in this field, failure rates are time variant. System is supposed to be unrepairable during life cycle. Finally, Continuous Time Markov Chain’s superiority in comparison with Monte Carlo method, both in accuracy and required amount of calculations is demonstrated and a few suggestions, based on obtained results, are presented for system reliability improvement.