Advanced MRI techniques have been increasingly applied in infants to explore the structural and functional architecture of the developing brain. Functional connectivity magnetic resonance imaging (fcMRI) utilises spontaneous, low-frequency, coherent fluctuations in blood oxygen level dependent signal to identify networks of functional cerebral connections. Application of fcMRI in infants provides unique technical challenges. To obtain high-quality fcMRI data, investigators have applied new technology and modified acquisition practices. Advanced analysis techniques have also been developed to improve anatomic registration, eliminate artifactual variance and improve signal-to-noise ratios. These measures have enabled successful, robust fcMRI investigations in neonates. Importantly, these methods are transferrable across institutions and clinical populations of interest. Neonatal fcMRI investigations have included healthy, term-born infants and prematurely-born infants with and without cerebral injury. In these populations, fcMRI data has been used to identify immature networks as early as 26 weeks postmenstrual age. These networks gradually mature. Prematurity (Figure 1) and white matter injury (Figure 2) significantly affect connectivity, altering network configuration and strength. These results demonstrate the promise of fcMRI as an investigational tool of neurodevelopment, providing insight into the earliest forms of functional cerebral development. While key groundwork has been laid, additional efforts are necessary to apply continued advances in technology and methodology. Expanded investigations will provide greater understanding of the processes underlying typical and atypical cerebral development and the role of these networks in neurodevelopmental outcomes.