Aerobic capacity plays a crucial role in football performance, making it a focal point in training processes. Small-sided games (SSGs) are widely used in football training, but the relationship between aerobic capacity and running performance during SSGs remains unclear. The aim of this study was to investigate possible correlations between maximum oxygen uptake (VO2max) and running performance in youth football players in SSGs (4:4, 3:3, 2:2, 1:1) with three different pitch sizes per player (150, 100, 75 m2/player). Sixteen male U15 football players participated in the study. Players underwent the Yo-Yo intermittent recovery test level 1, and their VO2max was estimated based on their performance. Subsequently, players participated in SSGs wearing GPS devices to measure internal and external load. Pearson or Spearman correlation was applied for statistical analysis depending on the normal distribution of the data. The results reveal that, for 4:4 and 3:3 relationships, larger pitches led to a greater impact of aerobic capacity (total distance (TD): 4:4, 150 m2/pl, r = 0.715, p = 0.002; 100 m2/pl, r = 0.656, p = 0.006; 75 m2/pl, r = 0.586, p = 0.017). In the 2:2 relationship, the opposite was observed, with more correlations appearing on smaller pitches (TD: 2:2, 100 m2/pl, r = 0.581, p = 0.018; 75 m2/pl, r = 0.747, p < 0.001). In the 1:1 relationship, correlations with VO2max, total distance, and speed were observed only on the larger pitch. In conclusion, the aerobic capacity of young football players can influence running performance indicators in SSGs. Therefore, aerobic capacity could serve as a criterion for team composition, making SSGs more competitive. Additionally, the variation in correlations in the 2:2 relationship and their limited presence in the 1:1 relationship may be attributed to technical-tactical factors, such as increased ball contacts and one-on-one situations typically occurring in smaller setups.