Acute intermittent hypoxia (AIH) elicits spinal respiratory motor plasticity, and has emerged as a promising therapeutic approach to restore lost respiratory (and non‐respiratory) motor function following cervical spinal cord injury (cSCI). Conversely, most individuals with cSCI experience sleep disordered breathing, generating chronic intermittent hypoxia (CIH) at intensities sufficient to trigger pathology. Since glia play a critical role in regulating neuroplasticity, they may play a key role in differentiating responses to therapeutic (AIH) versus pathogenic (CIH) intermittent hypoxia. Motor neuron‐microglial interactions regulate AIH‐induced phrenic motor plasticity. Specifically, phrenic motor neuron fractalkine, a chemokine unique to neurons released during hypoxia activates its high affinity receptor, CX3CR1—which is unique to microglia in the CNS. In response, microglia release ATP/adenosine, inhibiting AIH‐induced phrenic motor plasticity. Thus, if intermittent hypoxia or cSCI impact phrenic motor neuron fractalkine expression, they may directly impact plasticity and the potential of therapeutic AIH. In this study, we tested the hypothesis that phrenic motor neuron fractalkine expression is attenuated by daily AIH (but not CIH) in spinally intact rats, but not in rats with cSCI. Fractalkine was assessed in phrenic motor neurons of male rats with/without C2 hemisection (12 weeks post‐injury) exposed to 28 days of: 1) normoxia; 2) daily AIH (10, 5‐min episodes per day, 10.5% O2; 5‐min intervals); and 3) moderate CIH (2‐min 10.5% O2 episodes; 2‐min normoxic intervals; 8 hr/day). Fourteen days before hemisection, intrapleural Cholera toxin B injections were made to retrogradely label phrenic motor neurons. Fractalkine expression was assessed in 40 mm sections using a custom MATLAB algorithm to assess immunofluorescence optical density within labeled phrenic motor neurons. Spinally intact and injured rats have differential responses to daily AIH vs CIH. Whereas injured rats had no change in phrenic motor neuron fractalkine expression after daily AIH or CIH, fractalkine expression was marginally reduced in intact rats following daily AIH (p = 0.07; cohen’s d= 132%), but not CIH (p = 0.88; cohen’s d= 23%). Thus, daily (therapeutic) AIH may decrease motor neuron fractalkine and microglial adenosine release, thereby enhancing moderate AIH‐induced phrenic motor plasticity.