Summary The number of instationary 13C-metabolic flux (INST-MFA) studies grows every year, making it more important than ever to ensure the clarity, standardization and reproducibility of each study. We proposed CeCaFLUX, the first user-friendly web server that derives metabolic flux distribution from instationary 13C-labeled data. Flux optimization and statistical analysis are achieved through an evolutionary optimization in a parallel manner. It can visualize the flux optimizing process in real-time and the ultimate flux outcome. It will also function as a database to enhance the consistency and to facilitate sharing of flux studies. Availability and implementation CeCaFLUX is freely available at https://www.cecaflux.net , the source code can be downloaded at https://github.com/zhzhd82/CeCaFLUX. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]