Background: Little is known about morbidity patterns and healthcare utilization among specific Hajj pilgrim groups. This study examined influenza vaccination coverage, disease spectrum and healthcare utilization outcomes among Sudanese pilgrims during Hajj 2025. Methods: A cross-sectional analysis was conducted using de-identified patient records from the Saudi Health Electronic Surveillance Network for Sudanese Hajj pilgrims in 1–9 June 2025. Data included demographics, influenza vaccination status, healthcare utilization metrics, morbidities and temporal distribution of visits. Comparisons between hospital and primary healthcare center (PHC) attendees were performed using appropriate statistical tests. Results: A total of 1130 pilgrims sought care, with 88.6% (n = 1001) attending PHCs and 11.4% (n = 129) hospitals. Their mean age was 49.7 ± 12.9 years, and 67.9% (n = 767) were male. Influenza vaccination coverage was 79% (893/1130); vaccinated pilgrims had lower incidence of influenza-like illness (ILI) compared to unvaccinated pilgrims (5.2% vs. 15.2%, p < 0.01). Respiratory illnesses were the most frequent diagnoses (40.8% in PHCs and 24.8% in hospitals), followed by musculoskeletal disorders (24.5% and 16.3%, respectively). Compared to PHCs, presentation rate for chronic diseases was higher in hospitals (19.4% vs. 8.7%, p < 0.001), so was the median clinic time (14.1 vs. 8.6 min, p < 0.001). Healthcare utilization peaked on days 3–5 coinciding with the ‘Arafat Day’. Conclusions: Sudanese pilgrims most commonly presented with acute respiratory conditions, with PHCs managing the majority of cases, and influenza vaccination was protective against ILI. Findings emphasize the need for strong primary care, efficient resource allocation, and targeted preventive strategies to safeguard pilgrims’ health in the future.