This paper presents a preliminary numerical investigation on the design of the runner cone for a small turbine test rig under development at IIT Roorkee, India. The test rig is designed to study the formation and mitigation of rotating vortex rope (RVR) in the draft tube of a low head Francis turbine. The original runner cone design needs to be modified to include the provision for axial jet injection. Three different configurations, namely, a truncated cone and two original length cones with different nozzle positions, have been compared with the original cone to choose a suitable one for further investigations. The entire three-dimensional flow passage of the turbine unit has been simulated using the shear stress transport turbulence model after carrying out a mesh independence test on the original design. The proposed designs are compared at three different operating points. The amplitude and frequency of the pressure pulsations in the draft tube have been analyzed using the fast Fourier transform (FFT) method.