In this paper, we investigate the dynamics of a tethered flexible filament due to fluid flow inside a microchannel. We use the finite sized dissipative particle dynamics (FDPD) approach to model this problem. The flexible filament is modeled as a bead-spring system with both extensional and flexural rigidity. The influence of flow rate and bending stiffness on the filament dynamics is studied in terms of the different conformational modes obtained. The competing effects of the hydrodynamic force and elastic force in the presence of Brownian thermal effects of comparable order influence the mode shapes of the filament. The dynamics of the filament motions are further analyzed using proper orthogonal decomposition. An important consequence of the dynamics of the filament is that it causes cross-flow in the micro-channel, which could potentially be exploited in micro-mixing and pumping applications. The cross stream fluid transport is observed to be more pronounced for higher bending stiffness. © The Royal Society of Chemistry.