Background Cysteine proteinase inhibitor (cystatin, CPI) is one of the most important molecules involved in plant development and defense, especially in the regulation of stress responses. However, it is still unclear whether the Jatropha curcas CPI (JcCPI) gene functions in salinity response and tolerance. In this study, the sequence of the JcCPI gene, its expression pattern, and the effects of overexpression in Escherichia coli and Nicotiana benthamiana were examined. The purpose of this study was to evaluate the regulatory role of JcCPI in salinity stress tolerance. Results The CPI gene, designated JcCPI, was cloned from J. curcas; its sequence shared conserved domains with other plant cystatins. Based on a transcription pattern analysis, JcCPI was expressed in all tissues examined, but its expression was highest in the petiole. Additionally, the expression of JcCPI was induced by salinity stress. A potential role of JcCPI was detected in transgenic E. coli, which exhibited strong CPI activity and high salinity tolerance. JcCPI was also transferred to tobacco plants. In comparison to wild-type plants, transgenic plants expressing JcCPI exhibited increased salinity resistance, better growth performance, lower malondialdehyde (MDA) contents, higher anti-oxidase activity, and higher cell viability under salinity stress. Conclusions Based on the results of this study, overexpression of JcCPI in E. coli and N. benthamiana conferred salinity stress tolerance by blocking cysteine proteinase activity. The JcCPI gene cloned in this study will be very useful for the development of stress-tolerant crops.