Introduction Pembrolizumab, an immune-checkpoint inhibitor, is approved for first-line treatment of metastatic NSCLC in patients with tumours expressing programmed death-ligand 1 (PD-L1) with tumour proportion score (TPS) of ≥50%. We aimed to clarify some uncertainties regarding use of immunotherapy in patients with previous autoimmune (AI) disorders and assess real-world outcomes following treatment completion. Methods We performed a retrospective case record review of 82 patients with tumours expressing PD-L1 at TPS ≥ 50% and receiving first-line Pembrolizumab. Survival was estimated using the Kaplan Meier method. Results After 36.93 months (IQR: 34.37–40.20) median follow-up, median OS was 13.6 months (95% CI 8.9–19.3). There were 10 patients (12%) with AI co-morbidities and there was a trend toward improved median OS for this group versus those without AI comorbidity, 42 months (14.87-NR) versus 10.7 months (7.3–17.8), p = 0.073. Sixteen patients (20%) with nonprogressive disease at 2 years had significantly better median OS compared to those who did not complete 2 years of treatment, NR (42- NR) and 8.7 (5.8–14.1), p < 0.001. Immune related adverse events (irAE) of any grade occurred in 90% of the AI cohort compared with 70.8% of patients without AI comorbidity. Low grade adrenal insufficiency was the only irAE which occurred at a significantly higher rate in the AI group, p = 0.02. Conclusion Patients with previous AI diseases tolerate treatment well, and there is a non-significant trend for improved outcomes in this group. Patients who complete the course of pembrolizumab have significantly better survival outcomes than those who do not.