We present a comprehensive study of the stellar populations in two faint M31 dwarf satellites, And XI and And XIII. Using deep archival images from the Wide Field Planetary Camera 2 (WFPC2) onboard the Hubble Space Telepscope (HST), we characterize the horizontal branch (HB) morphologies and the RR Lyrae (RRL) populations of these two faint dwarf satellites. Our new template light curve fitting routine (RRFIT) detected RRL populations from both galaxies. The mean periods of $RR_{ab}$ (RR0) stars in And XI and And XIII are < $P_{ab}$ > = $0.621{pm}0.040$, and < $P_{ab}$ > = $0.648{pm}0.038$ respectively. Even though the RRL populations show a lack of $RR_{ab}$ stars with high amplitudes (Amp(V) > 1.0 mag) and relatively short periods ($P_{ab}$ ~ 0.5 days), their period - V band amplitude (P-Amp(V)) relations track the lower part of the general P-Amp(V) trend in the M31 outer halo RRL populations. The metallicities of $RR_{ab}$ stars were calculated via the [Fe/H]-log $P_{ab}$-Amp(V) relationship of Alcock et al. The metallicities thus obtained ($[Fe/H]_{And}$ $_{XI}=-1.75%$; $[Fe/H]_{And}$ $_{XIII}=-1.74$) are consistent with the values calculated from the RGB slope indicating that our measurements are not significantly affected by the evolutionary effects of RRL stars. We discuss the origins of And XI and And XIII based on a comparative analysis of the luminosity-metallicity (L-M) relation of Local Group dwarf galaxies.