The transition from late infancy into toddlerhood represents a fundamental period in early development. During this time, the prefrontal cortex (PFC) is undergoing structural and functional maturation processes that parallel the emergence and improvement of executive function skills, such as inhibitory control. Despite the importance of this developmental period, relatively little is known about the emergence and development of response inhibition, a form of inhibitory control, and the associated neural substrates across this key transition. Using functional near-infrared spectroscopy (fNIRS), an optical imaging technique suitable for imaging the developing brain, and an age-appropriate response inhibition task, we investigated the brain regions associated with response inhibition in 16-month-old toddlers. This pre-registered study extends our previous work with 10-month-old infants (Fiske et al., 2022) as it follows the same cohort of participants, now at 16 months of age. Whilst our previous work demonstrated that 10-month-old infants recruited right-lateralised regions of the PFC and parietal cortex when inhibition was required, the current study suggests that by 16 months, toddlers recruit the left superior parietal gyrus, the right inferior frontal gyrus, and bilateral regions of the dorsolateral PFC and orbital frontal cortex. Although there was no longitudinal change in response inhibition performance, more widespread, bilateral regions of the PFC were recruited during response inhibition at 16 months compared with 10 months. We acknowledge the need for replication of these results. Nevertheless, our findings suggest that the transition from infancy to toddlerhood may constitute an important period of reorganisation of the PFC that might support the development of early inhibitory control processes.