(1) Background: The exhaled fractional nitric oxide is a well-recognized biomarker used in clinical settings for controlling and managing asthma. Less is known about the value of Fractional Exhaled Nitric Oxide (FeNO) measurement in epidemiological studies on childhood asthma, although available evidence suggests that an increased FeNO is associated with an increased risk of asthma. (2) Aim: The aim of the study was to assess FeNO accuracy in the identification of children with asthma, participants in a population-based respiratory survey. (3) Material and methods: The cross-sectional study included 449 children, 224 (49.9%) boys and 225 (50.1%) girls aged 6−10 years. The FeNO was measured in 449 children; Spirometry tests were completed with 441 children, but technically acceptable spirometry was done in 350. All participants fulfilled the questionnaire (ISAAC) for assessment of the status of their respiratory system on which diagnosis was based on. FeNO and Spirometry were performed according to ERS/ATS recommendations. (4) Results: The FeNO was significantly higher in asthmatic children (n = 22): 27.3 ± 21.3 ppb; with allergic rhinitis (n = 106): 9.9 ± 21.6 ppb, with atopic dermatitis (n = 67) 20.8 ± 25.0 ppb, with an asthmatic tendency (n = 27): 19.8 ± 16.0 ppb in comparison to children without any respiratory/atopy symptoms. The highest diagnostic odds ratio and area under the curve were found in any treated asthma or asthma without any atopic symptoms in relation to FeNO cutoff > 35 ppb; DOR 4.85 and 8.37; AUC 0.615 and 0.795, respectively. The adjustment for spirometry parameters did not improve the diagnostic accuracy of FeNO. In each FeNO cutoff, there were more false positive than true positive subjects. (5) Conclusions. The best diagnostic accuracy of FeNO was for isolated asthma without any atopy against children without any coexisting respiratory or allergic disease. The sensitivity and specificity did not reach the required values for a good screening tool; therefore, it should not be used in epidemiological settings.