This study is aimed at determining the reproductive performance of anestrous ewes treated with nanoencapsulated GnRH after a progesterone-based protocol for estrus induction was proposed as a way of replacing eCG. A total of sixty anestrous, multiparous, non-lactating Barki ewes were randomly allocated into three homogenous groups and subjected to a CIDR-based estrus induction protocol. The first group (eCG) received an intramuscular (i.m.) injection of 350 IU of eCG at CIDR removal. The second (LNGnRH) and third (HLNGnR) groups received either 25 µg or 50 µg of encapsulated GnRH nanoparticles by the i.m. route in the form of spherical GnRH-encapsulated chitosan–TPP nanoparticles (which were 490.8 nm and had a 13.6 mV positive charge) 48 h after CIDR removal. Follicular dynamics, estrous behavior, luteal activity, and pregnancy outcomes were evaluated. Three days after CIDR removal, the number of large follicles increased by similar amounts in the LNGnRH and eCG groups and were significantly higher in both groups than in the HNGnRH group. However, no differences were observed in the numbers and diameters of CLs among the experimental groups and, on the other hand, treatment with HNGnRH significantly increased blood serum progesterone levels compared with eCG and LNGnRH. Treatment with HNGnRH increased conception, lambing, and fecundity rates (p < 0.05), with the trend of a higher litter size (p = 0.081) compared with eCG, whereas LNGnRH resulted in intermediate values. In conclusion, a dose of 50 µg of GnRH encapsulated in chitosan-TPP nanoparticles can be used as an alternative to eCG in progesterone-based estrus induction protocols in sheep.