Environmental toxins, endogenous metabolic products, and ionizing radiation can directly modify DNA or indirectly damage DNA through the generation of reactive oxygen and nitrogen species. Such DNA modifications can cause mutagenesis, aberrant gene expression, and cell death; DNA repair glycosylases, such as the NEIL family, are critical to the repair of various damages. We have extensively explored the ability of NEIL to excise damage from G-quadruplex (G4) structures, which are guanine-rich alternative DNA structures highly susceptible to oxidative DNA damage. Notably, G4s have been identified in promoter regions of oncogenes and tumor suppressor genes, and damaged G4s have been implicated in gene regulation. Understanding how NEIL processes damaged bases in G4 contexts can provide insight into the unique roles of NEIL beyond genome maintenance. We have conducted a thorough kinetic and binding affinity analysis of the repair of oxidized guanine lesions from different G4 sequences by NEIL1 and NEIL3. Our results showcase the interaction of NEIL with G4s and demonstrate the possible dynamic relationship between the NEIL family of enzymes, DNA repair, and gene regulation.