Infants born very preterm (<32 weeks of gestation) show distinct cognitive and motor problems throughout childhood. This study aims 1) to investigate differences in the structural connectome between very preterm born children and term born controls at school-age, and 2) to examine the relationship of the structural connectome with cognitive and motor problems. This study included 29 very preterm (12 males, mean age 8.6 years) and 52 term born peers (25 males, mean age 8.7 years). Wechsler Intelligence Scale for Children and Movement Assessment Battery for Children were used. Brain network measures of smallworldness, clustering coefficient and shortest path length based on fiber density of white matter tracts were determined from Diffusion Tensor Imaging data using probabilistic tractography. Smallworldness (F(1,79) = −2.09, p =.04, d = 0.52) and clustering coefficient (F(1,79) = −2.63, p =.01, d = 0.64) were significantly higher for very preterm children as compared to term peers. For Total Motor Impairment score and Manual Dexterity, there was a significant interaction between group and smallworldness (Beta = −10.81, p =.03 and Beta = −2.99, p =.004, respectively). Greater Total Motor Impairment and poorer Manual Dexterity were only significantly related to higher smallworldness in term controls (r = 0.35, p =.01 and r = 0.27, p =.04, respectively). Poorer Ball Skills were significantly related to higher smallworldness in both groups (Beta = −0.30, p =.03). This study clearly shows a more segregated network organization in very preterm children as compared to term peers. Importantly, motor problems go together with altered organization of the structural connectome in term born children, whereas this potential compensational process is only found for Ball Skills for very preterm children.