Background: There was a strict need to apply IMCI policy in public health units allover the developing countries. Objective: The study was designed to identify the challenges that have been faced the PHC physicians during the application of the IMCI policy, the level of adherence to its guidelines and difficulties in practicing its skills in relation to the IMCI training course received. Method: This study was conducted during the period February 2020 to May 2020 and included 349 physicians applying IMCI guidelines during the study period from whom data were collected using pre-designed questionnaire. Results: The most frequently reported significant difficulties in the IMCI case managing process were in classification of child's status (48.7%), evaluation of the child's status (30.7%), and guidance of caretaker (16%). A significant effect of the duration of IMCI training course on the perceived difficulties to practice skills of the IMCI case managing process was detected. Conclusion: The present study had announced the challenges during the application of IMCI policy in Sohag governorate, as perceived by physicians in the primary health care centers.