Organic electrochemical transistors (OECTs) based on conducting polymers have attracted significant attention in the field of biosensors. PEDOT:PSS and polyaniline (PANI) are representative conducting polymers used for OECTs. While there are many studies on PEDOT:PSS, there are not so many reports on PANI-based OECTs, and a detailed study to compare these two polymers has been desired. In this study, we investigated the fabrication conditions to produce the best performance in the OECTs using the above-mentioned two types of conducting polymers. Two main parameters were film thickness and film surface roughness. For PEDOT:PSS, the optimal conditions for fabricating thin films were a spin-coating rate of 3000 rpm and DI water immersion time of 18 hours. For PANI, the optimal conditions were a spin-coating rate of 3000 rpm and DI water immersion time of 5 seconds, and adding dodecylbenzenesulfonic acid (DBSA) was found to provide better OECT performances. The OECT performances based on PEDOT:PSS were superior to those based on PANI in terms of conductivity and transconductance, but PANI showed excellence in terms of film thickness and surface smoothness, leading to the good reproducibility of OECT performances.