Introduction: Fibromyalgia (FM) patients are known to have medical comorbidities. This study characterized the rates of infectious diseases in FM patients compared to the general population. Methods: A nationwide population-based case-control study was conducted, including all patients diagnosed with FM by a rheumatologist compared to a matched 5:1 control group within a large health maintenance organization in Israel (January 2002 to December 2023). Demographic, anthropometric, and health habit data were extracted from medical records as well as the ICD-9 codes of diagnoses related to infectious diseases in 9232 FM patients and 46,160 controls. Infection rates in the FM patients were compared to the controls over a mean follow-up of 6.7 years. Results: The FM patients had a significantly higher incidence of viral, bacterial, fungal, and parasitic diseases compared to the controls. The FM patients had significantly higher odds ratios (ORs) for respiratory/sinopulmonary infections, including upper respiratory tract infections (OR = 1.49), influenza (OR = 1.80), tonsillitis (OR = 1.40), sinusitis (OR = 1.98), otitis media (OR = 1.84), otitis externa (OR = 1.48), and pneumonia (OR = 1.60), all p < 0.01. They also experienced more gastrointestinal infections, including gastroenteritis (OR = 1.40), Helicobacter pylori (OR = 2.05), candidal esophagitis (OR = 7.88), and giardiasis (OR = 3.41), all p < 0.01. They had a higher prevalence of genitourinary infections, including urinary tract infections (OR = 1.79) and pelvic inflammatory disease (OR = 3.17), p < 0.01 as well as skin infections such as abscess (OR = 1.74) and cellulitis (OR = 1.64) and systemic infections such as symptomatic COVID-19 (OR = 1.76) and Cytomegalovirus (CMV) (OR = 1.85), all p < 0.01. Conclusions: The FM patients had a significantly higher incidence of infectious diseases than the general population. Further research is needed to better understand the underlying mechanisms and develop targeted interventions to address infection risks in FM patients.