The aim of this study was to determine the changes in physical performance and resting heart rate variability (HRV) in professional futsal players during the pre-season and in-season training periods. 11 athletes took part in the study (age=24.3+/-2.9 years; height=176.3+/-5.2 cm; weight=76.1+/-6.3 kg), and performed a repeated-sprint ability (RSA) test [6x40 m (20+20 m with a 180 degrees change of direction) sprints separated by 20 s of passive recovery] and Yo-Yo intermittent recovery test level 1 (Yo-Yo IR1) at 3 different moments (M1=beginning of pre-season; M2=end of pre-season; M3=mid in-season). The HRV indices were assessed at the same moments. After the short pre-season (3-week), mean RSA time (RSAmean) (M1=7.43+/-0.2 s; M2=7.24+/-0.2 s; P=0.003), decrement in RSA performance (RSAdecrement) (M1=6.7+/-0.3%; M2=5.0+/-0.9%; P=0.001), and Yo-Yo IR1 distance (M1=1.244+/-298 m; M2=1.491+/-396 m; P=0.002) were significantly improved (P<0.05). During the in-season (i. e., M3), performance in Yo-Yo IR1 and RSAmean were maintained. In contrast, RSAbest (M2=6.89+/-0.2 to M3=6.69+/-0.3; P=0.001) was improved and RSAdecrement (M2=5.0+/-0.9% to M3=6.6+/-0.9%; P=0.001) was impaired. At M2, there was an increase in HRV vagal-related indices compared with M1 that was maintained at M3. In conclusion, after a short pre-season, futsal players improved their RSA and Yo-Yo IR1 performance with concomitant improvements in HRV. These indices were maintained during the in-season period while RSAbest was improved and RSAdecrement impaired. Frequent monitoring of these performances and HRV indices may assist with identification of individual training adaptations and/or early signs of maladaption.