Many symptoms in multiple sclerosis (MS) can be related to changes in the levels of key neurotransmitters. These neurotransmitters have a direct role in the maintenance of neurons and also have immunomodulatory properties. Previously we have shown that when treatment began prior to the onset of clinical signs, daily treatment with the monoamine oxidase (MAO) inhibitor phenelzine (PLZ), which also elevates CNS levels of GABA, lead to substantial behavioral improvements in the experimental autoimmune encephalomyelitis (EAE), the animal model for MS. To determine whether PLZ could have beneficial effects in an already established disease state, we conducted experiments in which PLZ treatment only began when mice with EAE exhibited the first clinical signs of the disease. Using this more clinically relevant treatment approach, we find that PLZ treatment can reduce the severity of clinical signs and improve exploratory behaviors for the duration of the experiment in mice with EAE. Treatment with PLZ did not affect the infiltration of CD4+ T-cells into the spinal cord nor did it reduce the degree of reactive gliosis as measured by Iba1 immunostaining. Beginning PLZ treatment after the start of clinical signs did however lead to significantly better 5-HT innervation density in the ventral horn of the spinal cord and also resulted in higher levels of GABA, dopamine and norepinephrine in the brain and spinal cord. These results indicate that even in an established EAE disease state, PLZ can have clinical benefits. These benefits likely derive from PLZ's ability to normalize the innervation to ventral horn motor neuron pools as well as the elevations in GABA and biogenic amines that have been shown to have anti-inflammatory properties.