Despite their high sensitivity and rapid response characteristics, carbon nanotube (CNT) film-based gas sensors are plagued by bundle-induced poor gas selectivity and electrical noise. In this study, we developed thin-walled carbon nanotubes (TWCNTs) that were functionalized with a flavin mononucleotide (FMN) dispersant. This was done in order to reduce bundle size and enhance gas selectivity. Noncovalent functionalization with FMN has been demonstrated to improve CNT dispersion, minimize aggregation, and establish uniform electrical conduction pathways, thereby enhancing sensor stability. Gas sensing tests were conducted with NO2, CO2, and H2 (100 ppm each) to assess the selectivity of the sensor. The resistance change for NO2 was found to be four times higher than that for H2 and two times higher than that for CO2. This result indicates that the sensor exhibits improved selectivity. The riboflavin phosphate groups present on the modified CNTs provide additional adsorption sites and facilitate charge transfer processes. The combination of structural optimization, noise reduction, and superior selectivity exhibited by FMN-functionalized TWCNT sensors demonstrates their significant potential for high-performance gas detection, thereby establishing them as viable candidates for real-world applications.