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The configurational entropy is an indispensable tool to describe super-cooled liquids near the glass transition. Its calculation requires the enumeration of the basins in the potential energy landscape and when available, it reveals a direct connection with the relaxation time of the liquid. While there are several reports on the measurement of configurational entropy in passive liquids, very little is understood about its role in active liquids which have a propensity to undergo a glass transition at low temperatures. In this paper, we report a careful calculation of the configurational entropy in a model glass former where the constituent units are self propelled. We show that unlike passive liquids, the anharmonic contribution to the glass entropy in these self-propelled liquids can be of the same order as the harmonic contribution, and therefore must be included in the calculation of the configurational entropy. Our extracted configurational entropy is in good agreement with the generalized Adam-Gibbs relation predicted by the random first order transition theory enabling us to deduce a scaling relation between the configurational entropy and the point-to-set length scale in these active systems. Our findings could be of great utility in conventional active systems such as self-propelled granules, Janus particles and dense bacterial suspensions, to mention a few.