In this work, several ways to decrease the deactivation degree were proposed. To prevent local overheating, exfoliated graphite was used as a heat-conductive additive in catalyst composition. To decrease the deposition of heavy waxes, H-Beta zeolite was used for secondary reactions intensification and decreasing hydrocarbons chain length in the product. In this work, pelletized zeolite-containing cobalt catalyst with exfoliated graphite as a heat-conductive additive was investigated. The test run was 2200 h long and included continuous synthesis in a 6-meter high pilot reactor. The deactivation degree after 2200 h of the test run was 13%. The investigation of catalyst samples after synthesis by means of scanning electron microscopy showed that heavy hydrocarbons did not block the pore structure of catalytic pellets. Deactivation of cobalt catalyst was decelerated seriously due to zeolite-induced decrease in molecular weight of formed hydrocarbons. Investigation of catalysts before and after the test by means of transmission electron microscopy and X-ray diffraction analysis showed an increase in the size of clusters by 3–5 times, which is another important cause for catalyst deactivation. As a result, it was found that investigated cobalt catalyst for Fisher–Tropsch synthesis has a low deactivation rate. Its implementation in the industry can help gaining better economic performance for the synthetic fuel production process.