We have no systematic way of tracking job openings where MATSim knowledge is required or useful. The following contains advertisements that we got aware of.
Deadline 2016-fall: ARGUS Stadt- und Verkehrsplanung: Is looking for a student who could compare VISUM with MATSim for Hamburg, with possible longer term prospects. Details (German only).
Deadline 2016-08-29: Berliner Verkehrsbetriebe (BVG): The Berlin public transport authority BVG is offering a part-time job for students in the area of transport planning. Details (German only).
Deadline some time ago: Deutsche Bahn: The german railway company DB is offering an internship for microscopic modelling and simulation of public transport. Details (German only).
Please note that job-offerings are usually only available for a few weeks at most. So if the links above no longer work, it most likely means the jobs are no longer available.