Neural plasticity is a characteristic of the brain that helps it adapt to changes in sensory input. We hypothesize that auditory deafferentation may induce plastic changes in the cytoskeleton of the neurons in the inferior colliculus (IC). In this study, we evaluated the dynamic status of neurofilament (NF) phosphorylation in the IC after hearing loss. We induced auditory deafferentation via unilateral or bilateral cochlear ablation in rats, aged 4 weeks. To evaluate cytoskeletal changes in neurons, we evaluated mRNA fold changes in NF heavy chain expression, non-phosphorylated NF protein fold changes using SMI-32 antibody, and the ratio of SMI-32 immunoreactive (SMI-32-ir) neurons to the total neuronal population in the IC at 4 and 12 weeks after deafness. In the bilateral deafness (BD) group, the ratios of SMI-32-ir neurons significantly increased at 4 weeks after ablation in the right and left IC (6.1 ± 4.4%, 5.0 ± 3.4%, respectively), compared with age-matched controls (P < 0.01, P < 0.01). At 12 weeks after ablation, the ratio of SMI-32 positive neurons was higher (right, 3.4 ± 2.0%; left, 3.2 ± 2.3%) than that in the age-matched control group, albeit not significant in the right and left side (P = 0.38, P = 0.24, respectively). Consistent with the results of the ratio of SMI-32-ir neurons, SMI-32-ir protein expression was increased at 4 weeks after BD, and the changes at 12 weeks after bilateral ablation were not significant in the right or left IC. The age-matched control fold changes of NF mRNA expression after bilateral deafness were not significant at 4 and 12 weeks after deafness in right and left IC. Unilateral deafness did not induce significant change of NF mRNA expression, SMI-32-ir protein expression, and the ratio of SMI-32-ir neurons in the IC at 4 and 12 weeks after hearing loss. Bilateral auditory deafferentation induces structural changes in the neuronal cytoskeleton within the IC, which is prominent at 4 weeks after BD. The structural remodeling of neurons stabilized at 12 weeks after BD. Unlike BD, unilateral auditory deafferentation did not affect the dynamic status of NFs in the IC.