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Premature birth affects the developmental trajectory of the brain during a period of intense maturation with possible lifelong consequences. To better understand the effect of prematurity on brain structure and function, we performed blood‐oxygen‐level dependent (BOLD) and anatomical magnetic resonance imaging (MRI) at 40 weeks of postmenstrual age on 88 newborns with variable gestational age (GA) at birth and no evident radiological alterations. We extracted measures of resting‐state functional connectivity and activity in a set of 90 cortical and subcortical brain regions through the evaluation of BOLD correlations between regions and of fractional amplitude of low‐frequency fluctuation (fALFF) within regions, respectively. Anatomical information was acquired through the assessment of regional volumes. We performed univariate analyses on each metric to examine the association with GA at birth, the spatial distribution of the effects, and the consistency across metrics. Moreover, a data‐driven multivariate analysis (i.e., Machine Learning) framework exploited the high dimensionality of the data to assess the sensitivity of each metric to the effect of premature birth. Prematurity was associated with bidirectional alterations of functional connectivity and regional volume and, to a lesser extent, of fALFF. Notably, the effects of prematurity on functional connectivity were spatially diffuse, mainly within cortical regions, whereas effects on regional volume and fALFF were more focal, involving subcortical structures. While the two analytical approaches delivered consistent results, the multivariate analysis was more sensitive in capturing the complex pattern of prematurity effects. Future studies might apply multivariate frameworks to identify premature infants at risk of a negative neurodevelopmental outcome., To better understand the effect of prematurity on brain structure and function, we evaluated BOLD and anatomical MRI metrics in a set of 90 cortical and subcortical brain regions of 88 newborns at 40 weeks of postmenstrual age, with no evident radiological alterations and variable gestational age (GA) at birth. Data‐driven multivariate analyses of these measures were in agreement with univariate findings and indicated that GA at birth was associated with bidirectional and diffuse alterations of BOLD functional connectivity and more focal alterations of regional volume and BOLD activity (assessed through the fractional amplitude of low‐frequency fluctuation, fALFF). Future studies might successfully apply multivariate frameworks to identify premature infants at risk of a negative neurodevelopmental outcome.