Peripheral nerve injury (PNI) severs peripheral connections and induces profound reorganization of primary somatosensory (S1) and motor (M1) cortical maps, a dynamic process that critically shapes the extent and quality of functional recovery. Brain-derived neurotrophic factor (BDNF) has emerged as a central molecular hub linking the initial peripheral insult to subsequent central plastic changes. This review systematically examines BDNF-mediated cortical remodeling following PNI, with a particular emphasis on its spatiotemporally specific regulatory mechanisms and the therapeutic opportunities they present. Immediately after PNI, deafferented cortical territories undergo rapid functional silencing and, over time, become progressively encroached upon by adjacent intact representations. This maladaptive reorganization—characterized by sensory map fusion and motor compensatory invasion—actively impedes successful reinnervation and optimal recovery. Such phenomena have been consistently documented in both non-human primate models and human fMRI studies, spanning sensory and motor modalities. Motor remapping is also prominently observed in facial nerve injury and chronic nerve compression models, underscoring the universality of these plastic changes. Notably, a range of interventions including regional local anesthesia, auditory-tactile substitution, and guided tactile imagery can effectively mitigate this aberrant remodeling, revealing promising avenues for the therapeutic modulation of cortical plasticity during critical post-injury windows. BDNF coordinates post-PNI cortical remodeling through three mechanistically interconnected pathways. First, BDNF drives dendritic and axonal growth via TrkB receptor signaling: retrogradely transported axonal signaling endosomes integrate CREB-dependent transcriptional programs with mTOR-mediated local protein synthesis to bolster dendritic arborization and axonal elongation, while BDNF-induced Limk1 translation precisely fine-tunes actin cytoskeletal dynamics, thereby stabilizing dendritic spine morphology. Second, BDNF governs GABAergic interneuron maturation and perineuronal net formation through the JNK signaling cascade, thereby acting as a “plasticity brake” that preserves the delicate excitatory/inhibitory balance and constrains indiscriminate, maladaptive rewiring. Third, BDNF robustly potentiates NMDAR-dependent long-term potentiation (LTP) by elevating NMDA channel open probability and increasing synaptic receptor density, thus tightly coupling structural remodeling with functional synaptic strengthening. Concurrently, long-term depression pathways are subject to modulation, with NMDAR antagonism exerting time-dependent, bidirectional effects that vary with the post-injury phase. Superimposed on these mechanisms, the functionally antagonistic actions of proBDNF/p75NTR (favoring pruning and growth cone collapse) and mature BDNF/TrkB (promoting survival and stabilization) add further layers of regulatory complexity, highlighting the absolute necessity for precise spatiotemporal control in any therapeutic strategy. Extending our previous experimental findings, we introduce a “cortical reclamation threshold” model. In this framework, early upregulation of BDNF-TrkB signaling enhances inhibitory tone to restrict cortical encroachment by neighboring intact regions, whereas delayed but precisely timed BDNF delivery following surgical nerve repair actively facilitates the reclamation of the original, deafferented cortical maps by regenerating afferent fibers. Importantly, the common BDNF Val66Met polymorphism may significantly modulate individual thresholds, providing a biologically grounded rationale for patient stratification and personalized timing of intervention. Despite this mechanistic promise, clinical translation faces considerable hurdles. These include inherently poor pharmacokinetics of BDNF, severely limited penetration across the blood-brain barrier, dose-dependent neurotoxicity mediated through the p75NTR receptor, and the overarching dual-edged nature of BDNF signaling, which can simultaneously promote both adaptive and maladaptive plasticity. Emerging delivery platforms——including engineered exosomes, polymeric nanoparticles, cryogel microcarriers, and adeno-associated virus (AAV)-based gene therapy——offer potential solutions, but all require rigorous pharmacokinetic, toxicological, and functional validation. Future research priorities should encompass: (1) comprehensive single-cell and spatial transcriptomic mapping to resolve BDNF cellular sources and real-time signaling dynamics across distinct cortical layers and cell types; (2) genotype-stratified dose-response studies to establish safe, effective, and personalized delivery protocols; and (3) large-scale multicenter clinical trials that seamlessly integrate BDNF-targeted interventions with multimodal rehabilitation strategies, such as repetitive transcranial magnetic stimulation and mirror therapy, with longitudinal neuroimaging serving as a biomarker for cortical reclamation. By systematically addressing these priorities, we aim to transform BDNF from a critical endogenous regulator into a precisely controllable and titratable therapeutic target, ultimately enabling a paradigm shift from mere structural repair to true functional neural reconstruction following PNI.