People living with HIV (PLHIV) are prone to tuberculosis (TB) and hepatitis co-infections, which cause substantial burden on morbidity and mortality. However, data on the burden of HIV co-infection from a specific low- and middle-income country are limited. To address this gap in evidence, a meta-analysis of published literature and country surveillance report was conducted to estimate the burden of TB, hepatitis B (HBV) and hepatitis C (HCV) co-infection among PLHIV in Nepal. Twenty-three studies, including 5900 PLHIV, were included in the meta-analysis. The pooled prevalence of HIV-TB, HIV-HBV and HIV-HCV co-infection was 19% (95% CI, 10-28%), 3% (2-5%) and 19% (4-33%), respectively. Low CD4 cell count (pooled odds ratio [OR] 4.38, 95% CI 1.11-17.25), smoking (3.07, 1.48-6.37) and alcohol drinking (3.12, 1.52-6.43) were significantly correlated with HIV-TB co-infection. The odds of HCV co-infection was greater in PLHIV, who were male (5.39, 1.54-18.89) and drug users (166.26, 15.94-1734.44). PLHIV who were on antiretroviral therapy had a reduced risk of HCV co-infection (0.49, 0.36-0.66) than the general PLHIV population. The burden of TB and hepatitis co-infection among PLHIV in Nepal was high. Regular screening of PLHIV for co-infections and prompt initiation of treatment are essential to reduce the transmission of infection and improve quality of life.