The aim of the present paper is to discuss the boundary layer flow induced in a nanofluid due to a stretching permeable sheet in the presence of a magnetic field. Instead of no-slip boundary conditions, slips at the boundary have been considered. Casson fluid model was used to characterise the non-Newtonian fluid behaviour. The effects of Brownian motion and thermophoresis on heat and mass transfer were considered. Using similarity transformations, the governing partial differential equations were transformed into ordinary ones. The self-similar equations were then solved numerically using shooting technique with fourth order Runge-Kutta method. The solutions for velocity, temperature and concentration fields depended on the pertinent parameters. It was observed that the velocity decreased but the temperature and nanoparticle volume fraction increased with the increase of Casson fluid parameter. With the increase in velocity slip parameter as well as magnetic parameter, fluid velocity decreased. Due to increase in thermal slip, temperature decreased and with the increase in mass slip parameter, concentration also decreased. Temperature was found to increase but the nanoparticle volume fraction decreased due to the Brownian motion. On the other hand, temperature and nanoparticle volume fraction were both found to increase with the increase of thermophorosis parameter as well as with the increasing strength of magnetic parameter. Thus, velocity slip at the boundary and magnetic parameter acted as flow controlling parameters. It is believed that this type of investigation is very much helpful for the manufacturing of complex fluids and also for cleaning oil from surfaces.