Tremendous development in electronic devices and their indiscriminate use has created a severe problem of electromagnetic pollution. Different types of electromagnetic interference (EMI) shielding materials and structures are used to protect electronic devices from the harmful effect of electromagnetic pollution. A present study was conducted to compare the effect of dielectric and magnetic nanofillers on electromagnetic shielding effectiveness (EMI SE) of carbon fiber reinforced composite structures (CFRC). Composites structures were developed using different dielectric and magnetic nanofillers. Effect of nanofillers on microwave absorption properties and reduction in electromagnetic pollution was investigated. Relationship between electrical conductivity and EMI shielding effectiveness in L, S, C, and X-frequency range was also studied. Among the dielectric nanofillers, silicon carbide showed excellent EMI SE in X-frequency range, while among magnetic nanofillers, zinc oxide showed excellent EMI shielding characteristics in a broad frequency range of 100 MHz to 13.6 GHz. Among magnetic nanofillers, CFRC with zinc oxide nanofillers showed the lowest skin depth value of 3.32 × 10−4 mm and among dielectric nanofiller, CFRC with silicon carbide nanofillers gave the lowest skin depth value of 6.49 × 10−4 mm, implying their excellent potential in EMI shielding applications.