Abstract Background Intestinal parasitic infection is one of the parasitic infections affecting people living in prison. Helminths and intestinal protozoan infections are the most common parasitic infection that may cause serious life-threatening diseases in inmates living in developing countries. This study was aimed to investigate the prevalence and associated factors of intestinal parasitic infections (IPIs) among inmates living in Arba Minch prison, southern Ethiopia. Methods Institutional based cross sectional study was conducted on Arba Minch inmates, southern Ethiopian. Pre-tested semi-structured questionnaire was used to gather the data of socio-demographic characteristics, hygiene status of the prisoners, sanitation condition of the prison, and associated factors for IPIs by face to face interview. Direct wet-mount examination and formol-ether sedimentation techniques were used to examine intestinal parasitic infection from stool specimens. Binary logistic regression analysis was used to see the association between different variables and the IPI. Odds ratio with 95% CI was computed to determine the presence association and strength of the associated factors. Result A total of 320 prisoners were participated in this study. Of these, 154(48.1%) of them were infected with one or more intestinal parasites. Eight different intestinal parasites species were identified and Giardia lamblia was the predominant parasite. Among infected inmates, nearly one out of four of them had multiple parasitic infections dominated by Giardia lamblia and E. histolytica/dispar co-infection. Sleeping in group [AOR = 1.9; 95% CI: (1.0–3.8)], married prisoners [AOR = 1.8; 95% CI: (1.1–2.9)], and hand washing habits after handling soil [AOR = 2.4; 95% CI: (1.0–5.6)] were independently associated with IPI. Conclusion High prevalence of intestinal parasitic infection was detected in Arba Minch inmates, southern Ethiopian. Absence of hand washing, marital status, and way of sleeping were the factors associated with the IPI. Implementation of mass drug administration, education on water, sanitation and hygiene (WASH) and periodic screening of intestinal parasitic infection is very important to reduce the high prevalence IPIs in prison.