Perinatal brain injury is a significant cause of adverse neurodevelopmental outcomes. The objective of this systematic review was to identify patterns of altered brain function, quantified using functional connectivity (FC) changes in resting-state fMRI (rs-fMRI) data, that were associated with motor and language outcomes in individuals with a history of perinatal brain injury. A systematic search using electronic databases was conducted to identify relevant studies. A total of 10 studies were included in the systematic review, representing 260 individuals with a history of perinatal brain injury. Motor and language outcomes were measured at time points ranging from 4 months to 29 years 1 month. Relations between FC and motor measures revealed increased intra-hemispheric FC, reduced inter-hemispheric FC and impaired lateralization of motor-related brain regions associated with motor outcomes. Altered FC within sensorimotor, visual, cerebellum and frontoparietal networks, and between sensorimotor, visual, auditory and higher-order networks, including cerebellum, frontoparietal, default-mode, salience, self-referential and attentional networks were also associated with motor outcomes. In studies assessing the relationship between rs-fMRI and language outcome, reduced intra-hemispheric FC, increased inter-hemispheric FC and right-hemisphere lateralization of language-related brain regions correlated with language outcomes. Evidence from this systematic review suggests a possible association between diaschisis and motor and language impairments in individuals after perinatal brain lesions. These findings support the need to explore the contributions of additional brain regions functionally connected but remote from the primary lesioned brain area for targeted treatments and appropriate intervention, though more studies with increased standardization across neuroimaging and neurodevelopmental assessments are needed.