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Simple Summary: Coccidiosis, one of the most contagious diseases among domestic rabbits, negatively affects production and results in massive economic losses. This study evaluates the therapeutic efficacy of treatment with aqueous neem leaf extract and ethanolic pomegranate peel extract (PPE) individually and in combination on the intestinal coccidiosis caused by Eimeria spp. in New Zealand white and V-line (VL) rabbits. Rabbits from two breeds were divided into ten equal groups (five groups each for NZ and VL). All rabbits were inoculated with Eimeria spp. oocysts except for the rabbits in the first group (G1) (negative control). The remaining groups were: G2, positive control, G3, treated with neem leaf extract, G4, treated with pomegranate peel extract (PPE), and G5, treated with a combination of neem leaf extract and PPE. Our results showed that the use of neem leaf and/or pomegranate peel extract for both breeds resulted in improved growth performance, a significant reduction in mean oocyst count, no mortalities, an anticoccidial index > 120, and significantly improved economic efficiency measures when compared to the positive control group. Healthy, weaned, coccidial-free male rabbits from two breeds (New Zealand white (NZ) and V-line (VL)) were divided into 10 equal groups (5 groups each for NZ and VL) (3 replicates/group, 6 rabbits/replicate, 18 rabbits/group). All rabbits were inoculated with 5 × 104 Eimeria spp. oocysts (E. intestinalis (67%), E. magna (22%), and E. media (11%)) except for the rabbits in the first group (G1), which were inoculated with a sterile solution and served as a negative control. The remaining four groups were treated as follows: G2, no treatment/positive control, G3, treated with neem leaf extract, G4, treated with pomegranate peel extract (PPE), and G5, treated with a combination of neem leaf extract and PPE. For both breeds, our results showed that the use of neem leaf and/or pomegranate peel extract resulted in improved growth performance, with a significant improvement in relative feed conversion ratio (FCR) compared to the positive control groups, which recorded the worst values, as well as a significant (p ≤ 0.05) reduction in mean oocyst count compared to the positive control groups. We also observed downregulation of mRNA levels of IL-1βα, IL6, and TNF-α in the herbal treatment groups compared with the mRNA levels of these genes in the positive control groups. Herbal treatment with neem leaf and/or pomegranate peel extracts had positive effects on the NZ and VL rabbits experimentally infected with mixed Eimeria species, as evidenced by their healthy appearance, good appetite, no mortalities, an anticoccidial index > 120, and a significantly higher total return and net profit when compared to the positive control groups of both breeds. In NZ rabbits, the treatment with neem leaf extract alone (G3) or in combination with PPE (G5) recorded the most efficient economic anticoccidial activity. [ABSTRACT FROM AUTHOR]