Standard exhalation time for measuring fractional exhaled nitric oxide (FeNO) is 10 sec, but this is not easy for younger children. We aimed to investigate the agreement between FeNO values during 10-sec (FeNO-10) and 6-sec (FeNO-6) exhalation and the feasibility of measuring FeNO-6, using a hand-held analyzer, NIOX-MINO®. FeNO values measured during 10- and 6-sec (random order) were compared. Success rates of the two different time modes were also evaluated. In 119 asthmatic children (median age 8 years [range 4-15]) who had been already accustomed to NIOX-MINO®, median FeNO-10 (29 ppb [IQR 15.2-42.0]) and FeNO-6 (27 ppb [IQR 16.0-43.5]) did not differ significantly (P = 0.90), and there was a good correlation between both values (r = 0.984, P < 0.001). Mean difference (FeNO-10-FeNO-6) was -0.151 ppb (95% CI: -0.95 to 0.65, limits of agreement: -8.8 to 8.5). In 46 asthmatic children (median age 7 years [range 4-15]) who had never used any FeNO analyzers, all the children aged 8 years and more (n = 21) succeeded in measuring FeNO on both time modes, whereas for children aged younger than 8 years (n = 25) success rates of the 10- and 6-sec mode were 60.0% and 92.0%, respectively. In conclusion, we showed good agreement between FeNO-10 and FeNO-6, and the 6-sec mode of NIOX-MINO® is more feasible than 10-sec mode for measuring FeNO in younger children.