Synthetic fusion proteins have shown great potential in various biotechnological and (bio)pharmaceutical applications. They usually contain more than two protein domains joined by a linker peptide sequence which is often selected intuitively or in ad hoc manner. Thus, we developed an integrated web-based system, SynLinker, to provide appropriate linker candidates for constructing fusion proteins. We compiled a total of 2260 linker sequences comprising of natural linkers extracted from a set of non-redundant multi-domain proteins in Protein Data Bank and artificial/empirical linkers collected from literature and patents. Multiple query interface allows users to search for the desired linker candidates based on selection criteria and their preferences. In addition, a selected linker can be combined with two domain structures which are uploaded and appended at its N and C terminals, thereby predicting a de novo structure of the fusion protein. Hence, SynLinker can serve as a systematic tool for researchers who are interested in designing synthetic fusion proteins.