•Four kinds of fatigue crack nucleation modes were revealed for P/M FGH96 superalloy.•Microscopic mechanisms of the effects of the size and location of inclusions on LCF lifetime were investigated.•A modified model was proposed to quantify the inclusions effect on LCF lifetime. Powder metallurgy (P/M) nickel-based superalloy FGH96 is widely used for turbine discs in aero-engines. With an increasing trend towards powder metallurgy routes for turbine discs, undesired non-metallic inclusions comparable to the grain size are unavoidably introduced during the manufacturing process. In this study, a series of strain controlled low cycle fatigue (LCF) tests were conducted on the specimens cut from a P/M FGH96 turbine disc at elevated temperature. The microscopic mechanisms of the effects of the size and inclusion location on LCF lifetime were investigated by using scanning electronic microscope (SEM) with energy dispersive X-ray spectroscopy (EDS) for the fractographic analysis of specimens. It is revealed that the P/M FGH96 superalloy is sensitive to surface defects, such as surface scratches and surface inclusion; while the specimen for which the crack nucleates from internal inclusion usually has a longer fatigue lifetime due to smaller stress concentration at the crack tip. Moreover, the inclusion involving its location and size has a significant influence on the P/M FGH96 superalloy’s LCF lifetime. Then, a modified model was proposed to quantify the inclusion effect on the LCF lifetime. Finally, a probabilistic model based on Bayesian approach was formulated to describe the scattering in LCF lifetimes induced by random inclusions.