The present study investigates the effect of cylindricity error on the performance of hydrodynamic journal bearing systems. Two types of cylindricity errors of the journal, namely the drum shape distribution cylindricity error (DCE) and the saddle shape distribution cylindricity error (SCE), are considered. The Legendre–Fourier model is used to characterize the profile of each journal. Based on the nonlinear analysis method, the dynamic characteristics and stability of hydrodynamic journal bearing systems are analyzed. The results indicate that cylindricity error affects the system stability, and the effect is related to the type and level of the error. DCE used with a certain range of operating speed and load is not harmful and is even beneficial to the stability of hydrodynamic journal bearing systems; conversely, SCE decreases the system stability. When the Sommerfeld number is between 0.02 and 0.05, cylindricity errors have a minimal effect on the system stability. Additionally, the results indicate that the effect of cylindricity error on the bearing system is more significant than that of roundness error.