Backyard poultry is evolving as a fast-growing sector in recent times across the world. Apart from providing nutritional security, and livelihood to marginalized sector, also fulfils the demand for organic and welfare meat and eggs. However, the productivity is often challenged by incidences of diseases due to poor biosecurity and lack of vaccination. In this study, systematic review and meta-analysis were performed on the global prevalence of infectious diseases in backyard chickens. A total of 22 bacterial, viral, parasitic and fungal diseases were reported from 55 publications between 2000 and 2020 worldwide. Viral diseases were the most reported followed by bacterial and parasitic diseases. 61 out of 91 studies from 55 publications investigated seven major diseases: Avian influenza (AI), Newcastle disease (ND), infectious bronchitis (IB), Mycoplasma gallisepticum (MG), Mycoplasma synoviae (MS), Salmonella infection, and infectious laryngotracheitis (ILT). The overall pooled prevalence estimate for all the diseases worldwide was 33% (95% confidence interval (CI): 28–38). The pooled estimates for most reported viral diseases AI and ND were 12.5% (95% CI: 7–18) and 30% CI: 19–43), respectively. IBD (71% CI: 13–100), MS (76% CI: 67–85) and helminth infestations (72% CI: 44–93) were the highly prevalent diseases among viral, bacterial and parasitic infections, respectively. The continent wise pooled prevalence ranged from 17–32%. The present results will help in devising the best possible strategies to minimize the disease risk for commercial poultry and humans as well as for improving the productivity of backyard poultry farming.