The purpose of this study was to investigate the recruitment pattern of deep and superficial neck flexors evoked by three different cervical flexion exercises using muscle functional MRI. In 19 healthy participants, transverse relaxation time (T2) values were calculated for the longus colli (Lco), longus capitis (Lca), and sternocleidomastoid (SCM) at rest and following three exercises: conventional cervical flexion (CF), craniocervical flexion (CCF), and a combined craniocervical flexion and cervical flexion (CCF-CF). CCF-CF gave the highest T2 increase for all muscles. CCF displayed a significantly higher T2 increase for the Lca compared with the Lco and the SCM. When comparing the CCF and CF, no significant difference was found for the Lca, whereas the Lco and SCM displayed a higher T2 increase during CF compared with CCF. This study shows that muscle functional MRI can be used to characterize the specific activation levels and recruitment patterns of the superficial and deep neck flexors during different cervical flexion exercises. During CCF-CF, all synergists are maximally recruited, which makes this exercise useful for high-load training. CCF may provide a more specific method to assess and retrain Lca muscle performance compared with CF and CCF-CF. This study highlights the need to differentiate between the Lco and Lca when evaluating their function, since these results demonstrate a clear difference in activation of both muscles.