Display omitted •Milli fixed bed Fischer-Tropsch reactors exhibit fast and highly nonlinear dynamics.•Thermal runaway may occur with disturbance of coolant temperature and feed flowrate.•Forced periodic operation may enhance Fischer-Tropsch reactor performance.•Temperature control is crucial – advanced control systems are recommended. Dynamic performance of a milli-scale fixed bed reactor for Fischer-Tropsch synthesis (FTS) was studied using a dynamic pseudo-homogeneous 1D reactor model. The model uses detailed kinetics to describe the rates of FTS product formation. Dynamic responses of the process variables and main performance indicators, including productivity of C5+ hydrocarbons and CH4 selectivity, to input step changes, were analyzed. Total of 7 inlet variables were used in step-change-response analysis, with different magnitudes of change and for two initial steady-state conditions. Reactor simulations show highly nonlinear behavior due to phenomena coupling and fast dynamics due to system small scale and intensified rates within. In addition, reactor model shows instability related to thermal runaway with certain magnitudes of step change of coolant temperature and feed flow rate. The analysis outlines the effects of potential process disturbances on operation of milli-scale fixed bed reactor for FTS and provides general guidelines for control systems.