This paper investigates the influence of misaligned journal bearing effects on the thermally induced rotor instability (Morton effect “ME”) problem. The Morton effect is caused by uneven viscous heating of the journal in a fluid film bearing, which causes thermal bending, especially in rotors with an overhung disc or coupling weight. The thermally induced bending in the shaft may cause a vibration instability, which results in an excessive level of synchronous vibration. Previous research focused on parametric studies of the rotor and bearing design parameters, including overhung mass, bearing radial clearance, and lubricant viscosity. The present study investigates the influence of journal misalignment on the Morton effect. A coupled fluid-thermal-structural, three-dimensional finite element model (FEM) is developed to simulate fluid film pressures and temperatures, and shaft temperatures and vibrations. Simulations were conducted with different ratios of journal misalignment, and different pad-pivot types to determine their effect on the phenomenon. The simulation results indicate that the amplitude of the misalignment angle affects the instability speed range (ISR) caused by the Morton effect under certain conditions.