Molybdenum disulfide (MoS2) counter electrode (CE) is considered one of the most viable alternatives to Pt CE in dye-sensitized solar cells (DSSCs) owing to its abundance, low cost, and superior electrocatalytic activity. However, mostly, MoS2 CEs for DSSCs are prepared by conventional chemical reactions and annealing at a high temperature. By these conventional processes, deposition of sufficiently thin and transparent MoS2 layers is challenging; therefore, bifacial DSSCs employing transparent MoS2 CEs have not been studied. Here, we report transparent few-nanometer-thick MoS2 CEs prepared by atomic layer deposition at a relatively low temperature (98°C) for bifacial DSSC applications. MoS2 nanofilms with precisely controlled thicknesses of 3–16nm are conformally coated on transparent conducting oxide glass substrates. With increase in the MoS2 nanofilm thickness, the MoS2 CE electrocatalytic activity for the iodide/triiodide redox couple enhances, but its transparency decreases. Notably, the application of a thinner MoS2 nanofilm in a bifacial DSSC leads to lower conversion efficiency under front-illumination, but higher conversion efficiency under back-illumination. In particular, only the 3nm-thick MoS2 nanofilm shows reasonable photovoltaic performances under both front- and back-illumination conditions.