Electrodeposition of amorphous silicon thin films on Cu substrate from organic ionic electrolyte using pulsed electrodeposition conditions has been studied. Scanning electron microscopy analysis shows a drastic change in the morphology of these electrodeposited silicon thin films at different frequencies of 0, 500, 1000, and 5000 Hz studied due to the change in nucleation and the growth mechanisms. These electrodeposited films, when tested in a lithium ion battery configuration, showed improvement in stability and performance with an increase in pulse current frequency during deposition. XPS analysis showed variation in the content of Si and oxygen with the change in frequency of deposition and with the change in depth of these thin films. The presence of oxygen largely due to electrolyte decomposition during Si electrodeposition and the structural instability of these films during the first discharge-charge cycle are the primary reasons contributing to the first cycle irreversible (FIR) loss observed in the pulse electrodeposited Si-O-C thin films. Nevertheless, the silicon thin films electrodeposited at a pulse current frequency of 5000 Hz show a stable capacity of~805 mAh·g −1 with a fade in capacity of~0.056% capacity loss per cycle (a total loss of capacitỹ 246 mAh·g −1 ) at the end of 500 cycles.