Heart rate (HR) measurement is essential for children with abnormal heart beats. The purpose of this study was to determine whether HR measurement by smartphone applications (apps) could be a feasible alternative to an electrocardiography (ECG) monitor. A total of 40 children, median age of 4.3 years, were studied. Using four free smartphone apps, pulse rates were measured at the finger (or toe) and earlobe, and compared with baseline HRs measured by ECG monitors. Significant correlations between measured pulse rates and baseline HRs were found. Both correlation and accuracy rate were higher in the earlobe group than the finger/toe group. When HR was <120 beats per min (bpm), the accuracy rates were not different between the two different measuring sites for each app (median of 65 vs 76%). The accuracy rates in the finger/toe group were significantly lower than those in the earlobe group for all apps when HR was ≥ 120 bpm (27 vs 65%). There were differences among apps in their abilities to measure pulse rates. Taking children's pulse rate from the earlobe would be more accurate, especially for tachycardia. However, we do not recommend that smartphone apps should not be used for routine medical use or used as the sole form of HR measurement because the results of their accuracy are not good enough.