While the transition from the inspiratory to the post-inspiratory (post-I) phase is dependent on the pons, little attention has been paid to understanding the role of the pontine respiratory nuclei, specifically the Kölliker–Fuse nucleus (KF), in transitioning from post-I to the late expiratory (late-E) activity seen with elevated respiratory drive. To elucidate this, we used the in situ working heart-brainstem preparation of juvenile male Holtzman rats and recorded from the vagus (cVN), phrenic (PN) and abdominal nerves (AbN) during baseline conditions and during chemoreflex activation [with potassium cyanide (KCN; n = 13) or hypercapnia (8% CO2; n = 10)] to recruit active expiration. Chemoreflex activation with KCN increased PN frequency and cVN post-I and AbN activities. The inhibition of KF with isoguvacine microinjections (10 mM) attenuated the typical increase in PN frequency and cVN post-I activity, and amplified the AbN response. During hypercapnia, AbN late-E activity emerged in association with a significant reduction in expiratory time. KF inhibition during hypercapnia significantly decreased PN frequency and reduced the duration and amplitude of post-I cVN activity, while the onset of the AbN late-E bursts occurred significantly earlier. Our data reveal a negative relationship between KF-induced post-I and AbN late-E activities, suggesting that the KF coordinates the transition between post-I to late-E activity during conditions of elevated respiratory drive.