Preterm birth is a neurodevelopmental risk condition often associated with cognitive control (CC) impairment. Recent evidence showed that CC can be implicitly adapted through associative learning. In the present study we investigated the ability to flexibly adjust CC as a function of implicit stimulus-response temporal regularities in preterm (PT; N = 21; mean age 8 ± 1.3 years; gestational age 30 ± 18.5 weeks) and full-term (FT; N = 20; mean age 8 ± 1.3 years) school-age children. All children underwent an HD-EEG recording while undergoing the Dynamic Temporal Prediction (DTP) task, a simple S1–S2 detection task purposely designed to generate local-global temporal predictability of imperative stimuli. The Wisconsin card sorting test (WCST) was administered to measure explicit CC. The PT group showed more premature and slower (DTP) as well as perseverative (WCST) responses than the FT group. Moreover, pre-terms showed poor adaptive CC as revealed by less efficient global response-speed adjustment. This behavioral pattern was mirrored by a reduced and less sensitive to global manipulation anticipatory Contingent Negative Variation (CNV) and by different cortical source recruitment. These findings suggest that implicit CC may be a reliable endophenotypic marker of atypical cognitive development associated with preterm birth.