Cystic Echinococcosis (CE) is a neglected tropical disease (NTD) impacting the health and economy of the developing states including Pakistan. It is mainly caused by Echinococcus granulosus and renders huge economic losses to the livestock sector. This study investigated the prevalence of CE and associated risk factors. A total of 503 samples from food animals (including 226 cows, 102 buffaloes, 98 sheep, and 77 goats) were inspected for the presence of hydatid cysts by conducting postmortem at various slaughterhouses in district Narowal-Pakistan. Fertility and viability of collected hydatid cysts were assessed by microscopy and confirmatory diagnosis was obtained through conventional Polymerase Chain Reaction (PCR). A pre-structured questionnaire was used to collect baseline data in order to identify the associated risk factors with CE. An overall prevalence of 8.15% was found while in each species it was 12.83% in cattle, followed by buffalo (6.86%), sheep (4.08%) and goat (1.29%), respectively. The order of infection was highest in liver (35.71%) followed by lungs (33.33%) and then both organs at the same time (20%). Such epidemiological findings could help in developing preventive strategies and control programs for CE in Pakistan and other developing countries.