Background A free running asthma screening test is usually used for screening exercise-induced bronchoconstriction. The total serum allergen IgE level can reveal the patient's atopy characteristics. Our study is to evaluate the diagnostic values of the combination of the two tests in asthmatic children and compare this new diagnostic method with the International Study of Asthma and Allergies in Childhood (ISSAC) questionnaires and the bronchial provocation test, which are popular diagnostic tool for pediatric asthma. Methods A total of 773 school children were recruited in this study. The children's asthma was diagnosed by means of a combination of the free running asthma screening test and total serum allergen IgE level. The new diagnostic method value was assessed using receiver operating characteristic (ROC) curves and compared with other diagnostic tools such as ISSAC questionnaires and the bronchial provocation test. Results The AUC of this new diagnostic method was higher than 0.9. When the cut-off value of total serum allergen IgE level was >= 47 KU/L, the sensitivity and the specificity were 71.4% and 85.1%, respectively, which were better than those of either the ISSAC questionnaires or bronchial provocation test. Conclusion The combination of the free running asthma screening test and total serum allergen IgE level may be an effective diagnostic tool for children's asthma.