There is a need to explore less laborious point-of-care assessment tools to diagnose protein energy wasting (PEW) in children with chronic kidney disease (CKD). This cross-sectional study was undertaken to assess the profile of specific nutrition-focused physical examination (NFPE) and mid-arm muscle area (MAMA) in children with CKD and determine their role in the diagnosis of PEW. PEW criterion was applied to all eligible children and MAMA was derived from mid-arm circumference and triceps skin fold thickness. NFPE signs examined were muscle wasting (MW) and subcutaneous fat loss (FL). One hundred and twenty-six children with CKD (86 in CKD stages 2-4 and 40 on dialysis) were studied. PEW was prevalent in 41.8% children with CKD2-4 and in 72.5% on dialysis. In children with CKD 2-4, low MAMA, MW, and FL were significantly associated with PEW with an odd's ratio of 5.3 (1.55,18.30), 10.6 (3.8,29.8), and 10.5 (3.7,29.2) respectively (P = <0.001). Similarly, in children on dialysis, low MAMA, MW, and FL were more likely to be associated with PEW with an odd's ratio of 17 (2.2,127.7); P = 0.017, 16.6 (3,90.8); P = 0.001 and 19 (2.1,170.3); and P = 0.009, respectively. MW demonstrated high sensitivity and specificity [80.6 and 72%, respectively, with a positive predictive value (PPV) of 67.4%] to diagnose PEW in the CKD 2-4 group and in those on dialysis [86.2 and 72.1%, respectively, with PPV of 89.3%]. Clinical signs based on NFPE are useful in detecting PEW in children with CKD2-4 and in those on dialysis.