Recently, we demonstrated that endogenous feline leukemia virus (enFeLV) loads may vary among cats of different populations and that FeLV-infected cats have higher enFeLV loads than uninfected cats. Thus, we hypothesized that enFeLV might influence the pathogenesis and outcome of FeLV infection. No significant difference in the infection outcome (regressive versus progressive infection) was observed between groups of cats with high or low enFeLV loads following FeLV-A challenge. However, cats with high enFeLV loads showed higher viral replication (plasma viral RNA and p27 antigen levels) than cats with low enFeLV loads in the early phase of the infection. The enFeLV transcription level varied at different time points, but no clear-cut pattern was observed. In conclusion, our results demonstrated an association between enFeLV loads and FeLV replication but not outcome of infection. enFeLV should be considered as an important confounder in experimental FeLV infection or vaccination studies.