The present study examined cardiovascular adaptations in 8–10-year-old schoolchildren after a full school year (10 months) of 5 × 12 min/wk. of intense physical training, including small-sided ball games (soccer, basketball and floorball) or interval running. The study involved 8–10-year-old healthy Danish schoolchildren (n = 232), who were cluster-randomized to a small-sided games group (SSG, n = 60), an interval running group (IR, n = 57) or a control group (CON, n = 115). Comprehensive transthoracic echocardiography, resting heart rate and blood pressure measurements were performed at baseline and post intervention. For interval running, analysis of baseline-to-10-months changes showed significant (P < 0.05) between-group differences in delta scores for diastolic blood pressure (BP) and mean arterial BP (IR −3.2 ± 5.7 and − 2.2 ± 6.5 mmHg vs. CON 0.2 ± 5.3 and 0.4 ± 6.4 mmHg, respectively). Delta scores also showed a trend for reduction of mean arterial BP in SSG compared to CON (−2.1 ± 6.0 vs. 0.2 ± 5.3 mmHg, P = 0.067). Moreover, there were between-group differences in delta scores (P < 0.05) for selected echocardiographic parameters, i.e. in SSG vs. CON for interventricular septum thickness and peak transmitral flow velocity in early diastole, and in IR vs. CON for left ventricular systolic diameter. In conclusion, 10 months of 5 × 12 min/wk. of IR in 8–10-year-old children decreased diastolic BP, while both IR and SSG elicited cardiac adaptations. The results suggest that frequent low volume, intense physical training can have effects on the cardiovascular health profile in healthy children.