Ethiopia has adopted the Integrated Community Case Management of Newborn and Child Illness (iCMNCI) strategy to expand access to neonatal and child health services. This study assessed compliance with the iCMNCI case management protocol at the primary care settings. A descriptive cross-sectional assessment was conducted in eight districts of Benishangul-Gumuz Region from April to December 2019, and 1,217 sick children aged 2 to 59 months and 43 sick young infants aged 0 to 2 months who sought clinical consultation at the 236 health posts were selected purposively. Trained supervisors reviewed the medical records of two most recent cases from each illness category to quantify the extent to which health workers correctly assessed, classified, treated, and followed up cases per the iCMNCI guidelines. A total of 32,981 children sought clinical consultation of whom 31,830 (96.5%) were aged 2 to 59 months, and 1,151 (3.5%) were young infants aged 0 to 2 months. Of the 1,217 selected children, 426 (35%) had pneumonia, 287 (23.6%) malaria, 501 (41.2%) diarrhea, and 3 (0.2%) had malnutrition. Nearly two-thirds 306 (72%) of pneumonia cases were correctly classified as having had the disease and 297 (70%) were correctly treated for pneumonia; 213 (74%) were correctly classified as having had malaria and 210 (73%) were correctly treated for malaria; and 393 (78%) were correctly classified as having had diarrhea and 297 (59%) were correctly treated for diarrhea. Generally, the current practices of child illness assessment, classification, and treatment have deviated from iCMNCI guidelines. Future interventions should support frontline health workers to comply strictly with case management protocols through training, mentorship, and supervision.