Purpose To compare deoxygenation of the sternocleidomastoid, scalenes, and diaphragm/intercostals (Dia/IC) during submaximal intermittent neck flexion (INF) versus submaximal inspiratory threshold loading (ITL) in healthy adults. Methods Fourteen participants performed a randomized, cross-over, repeated measures design. After evaluation of maximal inspiratory pressures (MIP) and maximum voluntary contraction (MVC) for isometric neck flexion, participants were randomly assigned to submaximal ITL or INF until task failure. At least 2 days later, they performed the submaximal exercises in the opposite order. ITL or INF targeted 50 ± 5% of the MIP or MVC, respectively, until task failure. Near-infrared spectroscopy (NIRS) was applied to evaluate changes of deoxy-hemoglobin (ΔHHb), oxy-hemoglobin (ΔO2Hb), total hemoglobin (ΔtHb), and tissue saturation of oxygen (StO2) of the sternocleidomastoid, scalenes, and Dia/IC. Breathlessness and perceived exertion were evaluated using Borg scales. Results Initially during INF, sternocleidomastoid HHb slope was greatest compared to the scalenes and Dia/IC. At isotime (6.5–7 min), ΔtHb (a marker of blood volume) and ΔO2Hb of the sternocleidomastoid were higher during INF than ITL. Sternocleidomastoid HHb, O2Hb, and tHb during INF also increased at quartile and task failure timepoints. In contrast, scalene ΔO2Hb was higher during ITL than INF at isotime. Further, Dia/IC O2Hb and tHb increased during ITL at the third quartile and at task failure. Borg scores were lower at task failure during INF compared to ITL. Conclusion Intermittent INF induces significant metabolic activity of the sternocleidomastoid and a lower perception of effort, which may provide an alternative inspiratory muscle training approach for mechanically ventilated patients.