The aim of this study was to evaluate the effect of carbohydrate supplementation on free plasma DNA and conventional markers of training and tissue damage in long-distance runners undergoing an overload training program. Twenty-four male runners were randomly assigned to two groups (CHO group and control group). The participants were submitted to an overload training program (days 1-8), followed by a high-intensity intermittent running protocol (10 × 800 m) on day 9. The runners received maltodextrin solution (CHO group) or zero energy placebo solution as the control equivalent before, during, and after this protocol. After 8 days of intensive training, baseline LDH levels remained constant in the CHO group (before: 449.1 ± 18.2, after: 474.3 ± 22.8 U/L) and increased in the control group (from 413.5 ± 23.0 to 501.8 ± 24.1 U/L, p < 0.05). On day 9, LDH concentrations were lower in the CHO group (509.2 ± 23.1 U/L) than in the control group (643.3 ± 32.9 U/L, p < 0.01) post-intermittent running. Carbohydrate ingestion attenuated the increase of free plasma DNA post-intermittent running (48,240.3 ± 5,431.8 alleles/mL) when compared to the control group (73,751.8 ± 11,546.6 alleles/mL, p < 0.01). Leukocyte counts were lower in the CHO group than in the control group post-intermittent running (9.1 ± 0.1 vs. 12.2 ± 0.7 cells/µL; p < 0.01) and at 80 min of recovery (10.6 ± 0.1 vs. 13.9 ± 1.1 cells/µL; p < 0.01). Cortisol levels were positively correlated with free plasma DNA, leukocytes, and LDH (all r > 0.4 and p < 0.001). The results showed that ingestion of a carbohydrate beverage resulted in less DNA damage and attenuated the acute post-exercise inflammation response, providing better recovery during intense training.