With rapidly advancing technologies such as IoT, AI, robotics, and others, smart agriculture in Japan has been introduced and tested throughout the country. The validity of the implementation of smart agriculture could be measured by using cost analysis, working capacity assessment, and management efficiency analysis. In this study, we focused on pest-control management, wherein unmanned aerial vehicles (UAVs) for crop spraying have been recently introduced. In order to clarify the validity of UAVs for rice fields in Japan regarding costs and performance, we conducted a comparative study of pest-control sprayers, specifically: (1) tractor- mounted boom sprayers, (2) remote-control spraying helicopters (RC helicopters), and (3) UAVs. We estimated pest-control costs and the working capacity of each method. We also evaluated the management efficiency of 21 case scenarios of different pest-control sprayers and field areas ranging from 0.5 to 30 ha using data envelopment analysis (DEA) based on an input-oriented model. We used the input of pest-control cost and the output of gross farm income and surplus working capacity. Pest-control costs per unit area of boom sprayers, RC helicopters, and UAVs were approximately 925,597 yen/ha (US $8819/ha), 6,924,455 yen/ha (US $65,975/ha), and 791,724 yen/ha (US $7543/ha), respectively. The working capacity during pest-control scheduled days was 120, 195, and 135 ha, respectively. DEA results suggested that UAVs would be more efficient than boom sprayers and RC helicopters for the analyzed cases. UAVs for crop spraying showed relatively low cost and high management efficiency compared to the boom sprayers and RC helicopters; hence UAVs could be a suitable replacement to save cost and time.