Background The World Health Organization (WHO) launched a guideline in 2015 for managing Possible Serious Bacterial Infection (PSBI) when referral is not feasible in young infants aged 0–59 days. This guideline was implemented across 303 Basic Health Unit (BHU) Plus primary health care (PHC) facilities in peri-urban and rural settings of Sindh, Pakistan. We evaluated the implementation of PSBI guideline, and the quality of care provided to sick young infants at these facilities. Methods Thirty (10%) out of 303 BHU Plus facilities were randomly selected for evaluation. A survey team visited each facility for one day, assessed the health system support, observed the management of sick young infants by health care providers (HCP), validated their management, interviewed HCPs and caretakers of sick infants. HCPs who were unable to see a young infant on the day of survey were evaluated using pre-prepared case scenarios. Results Thirty (100%) BHU Plus facilities had oral amoxicillin, injectable gentamicin, thermometers, baby weighing scales and respiratory timers available; 29 (97%) had disposable syringes and needles; 28 (93%) had integrated management of childhood illness (IMCI)/PSBI chart booklets and job aids and 18 (60%) had a functional ambulance. Each facility had at least one HCP trained in PSBI, and 21 (70%) facilities had been visited by a supervisor in the preceding six months. Of 42 HCPs, 19 (45.3%) were trained within the preceding 12 months. During the survey, 26 sick young infants were identified in 18 facilities. HCPs asked about history of breastfeeding in 23 (89%) infants, history of vomiting in 17 (65%), and history of convulsions in 14 (54%); weighed 25 (97%) infants; measured respiratory rate in all (100%) and temperature in 24 (92%); assessed 20 (77%) for movement and 14 (54%) for chest indrawing. HCPs identified two infants with fast breathing pneumonia and managed them correctly per IMCI/PSBI protocol. HCPs identified six (23%) infants with clinical severe infection (CSI), two of them were referred to a higher-level facility, only one accepted the referral advice. Only one CSI patient was managed correctly per IMCI/PSBI protocol at the outpatient level. HCPs described the PSBI danger signs to eight (31%) caretakers. Caretakers of five infants with CSI and two with pneumonia were not counselled for PSBI danger signs. Five of the six CSI cases categorized by HCPs were validated as CSI on re-examination, whereas one had pneumonia. Similarly, one of the two pneumonia patients categorized by HCPs had CSI and one identified as local bacterial infection was classified as CSI upon reexamination. Conclusion Health system support was adequate but clinical management and counselling by HCPs was sub-optimal particularly with CSI cases who are at higher risk of adverse outcomes. Scaling up PSBI management is potentially feasible in PHC facilities in Pakistan, provided that HCPs are trained well and mentored, receive refresher training to appropriately manage sick young infants, and have adequate supplies and counselling skills.