Spinal cord injury (SCI) can cause permanent dysfunction proceeding from multifaceted neuroinflammatory processes that contribute to damage and repair. Fidgetin-like 2 (FL2), a microtubule-severing enzyme that negatively regulates axon growth, microglial functions, and wound healing, has emerged as a potential therapeutic target for central nervous system injuries and neuroinflammation. To test the hypothesis that FL2 knockdown increases acute neuroinflammation and improves recovery after SCI, we examined the effects of nanoparticle-encapsulated FL2 siRNA treatment after a moderate contusion SCI in rats. SCI significantly increased FL2 expression in the lesion site and rostral to the lesion 1 day post-injury (dpi). A single treatment of FL2 siRNA after injury led to modestly improved locomotor recovery consistent with the preservation of corticospinal tract function, accompanied by reduced inflammation and increased presence of oligodendrocytes. In determining the acute effects of treatment, RNA sequencing and gene set enrichment analyses revealed that FL2 siRNA modulates early cellular responses, including chemokine signaling, both pro- and anti-inflammatory immune reactions, and neurotransmitter signaling pathways at 1, 4, and 7 dpi. Follow-up analyses at 4 dpi using dual in situ hybridization and immunohistochemistry demonstrated that SCI increased FL2 mRNA and that FL2 was colocalized with microglia/macrophages. FL2 downregulation resulted in a marked accumulation of microglia at the lesion site, accompanied by increased inflammatory markers (IL-1β, TGF-β1, and CD68). The results suggest SCI induces an increase in FL2 expression that undermines acute inflammatory responses as well as spinal cord integrity and growth. Overall, our study suggests that targeting FL2 holds promise as a therapeutic strategy for treating SCI.