Objectives The Yale observation scale (YOS), also called the Acute Illness Observation Scale, was developed to help detect serious illness in febrile children. We conducted this study to evaluate the clinical utility of the YOS for predicting serious illness in Japanese primary care settings. Method We conducted a prospective observational study from June 2015 to January 2018. We enrolled patients younger than 10 years, who attended the primary care centre at the Aichi Medical University Hospital and who had recorded YOS scores. Serious illnesses included invasive bacterial infections and any conditions requiring artificial ventilation, surgical treatment, or cardiopulmonary resuscitation. We calculated point estimates for YOS sensitivity and specificity for predicting serious illness and hospitalisation. We evaluated the area under the receiver operating characteristic curve (AUC) by the Youden index. Results The 260 participants (227 outpatients and 33 inpatients) had a median age of 1.75 years (range, 0–10); 80 (30.8%) were younger than 1 year, 131 (50.4 %) between 1 and 3 years, 44 (16.9%) between 4 and 7 years, and 5 (1.9%) between 8 and 10 years. Infectious illness was the most common diagnosis (n = 211), followed by allergic disease (n = 11) and trauma (n = 10). Among the 211 patients with infectious illness, upper respiratory tract infections were the most common (n = 55). Fourteen patients among the 29 with YOS >10, and 19 among those with YOS ≤10 were hospitalised. We found 6 patients with serious illnesses: intussusception (n = 1; YOS, 22), encephalitis (n = 1; YOS, 16) and urinary tract infection (n = 4; YOSs, 18, 16, 8 and 6). The sensitivity and specificity of the YOS for predicting serious illness at a cut-off point of 10 were 0.67 and 0.90, respectively. The corresponding values for hospitalisation at that cut-off point were 0.42 and 0.93, respectively. The AUCs of the YOS for predicting serious illness and hospitalisation were 0. 82 (excellent) and 0.74 (acceptable). Conclusions We conclude that a YOS >10 may be useful to predict severe paediatric diseases in Japanese primary care settings.