BACKGROUND: Neonatal intestinal obstruction is the most common surgical emergency in the neonatal period. It is a life-threatening condition with high mortality especially in developing countries. There is limited study on treatment of neonatal intestinal obstruction and its accosted factors in Ethiopia, especially in TGSH and FHCSH. OBJECTIVES: To determine the type, treatment outcome and associated factors of intestinal obstruction in neonates admitted with NIO at TGSH and FHCSH pediatrics department, NICU from January 2017 to January 2020. METHODS: An institution based cross sectional study was conducted using chart review of neonates with intestinal obstruction admitted at NICU of TGSH and FHCSH. One hundred fifty neonates with intestinal obstruction were included in the study and check list was used to collect the data by revising the charts. The collected data was entered, cleaned and analyzed using SPSS version 23. Crude and adjusted odd ratio with 95% CI were calculated to determine the strength of association between the dependent and independent variables. A p-value less than 0.05 was considered as statistically significant in all of the analyses. RESULT: One hundred fifty neonates with intestinal obstruction were studded; out of this 85.3% were survived and magnitude of poor treatment outcome or (death rate) was 14.7%. Regarding to the type intestinal obstruction, 42.0% were Hirschsprung disease, 32.7% were ARM, 23.3% were intestinal atresia and 2.0% were others. Associated congenital anomalies AOR=11.02 (2.10-57.82) of 95%CI, preoperative sepsis AOR=6.06(1.36-27.01) of 95%CI and low birth weight AOR=4.34(1.04-18.57) of 95%CI were associated factors with poor treatment outcome respectively. From intestinal obstruction intestinal atresia was associated with poor treatment outcome AOR= 4.98(1.09-22.78) of 95%CI. CONCLUSION: in this study high case fatality rate was observed and congenital anomalies, preoperative sepsis and low birth weight are significantly associated with poor treatment outcome. Early detection and management of preoperative sepsis is important. Keyword; Treatment outcome, Neonatal intestinal obstruction, associated factors, Bahir Dar