The aim of this study was to investigate variations in cognitive performance and difficulty perception in 9-10-year-old boys. Fifteen healthy boys (Age = 9.8 ± 0.4 years; Height = 146 ± 5.2 cm; Body mass = 34.2 ± 2.9 kg) performed three cognitive tasks, the reaction time (RT), the trail-making test, TMT (to evaluate flexibility), and the barrage tests (to evaluate selective attention [SA]). The tests were performed at 07:00 and 17:00 h. The results demonstrated that oral temperature, RT, and flexibility were significantly higher at 17:00 h than at 07:00 h. A significant main effect of diurnal variation was found for RT (t = 3.075, p = 0.008), SA (t = 2.43, p = 0.029), and executive function (TMT, Parts A and B) (t = 5.86, p < 0.001; t = 4.85, p < 0.001, respectively). However, these rhythms of cognitive performance were not correlated with the rhythm of core temperature at 07:00 h. In conclusion perceived difficulty was correlated with executive function in situations with higher level of difficulties.