Shrimp trawl fishery is of significant importance in Saudi Arabia’s marine capture fishery sector. Al Qunfudhah and Jizan are the only ports along the southern Saudi Arabian coast of the Red Sea dedicated to shrimp fishing. This study evaluates the catch per unit effort (CPUE) of targeted shrimp species along with the associated retained bycatch and discard ratios across these two trawling locations. Using daily catch data from commercial shrimp trawlers specific to each port’s vessel type, this research provides the first comprehensive analysis of CPUE dynamics and fishing practices in these fishing grounds. The CPUE of target shrimps exhibited a wide range (0.01 kg h−1 to 13.08 kg h−1) with an overall mean of 1.37 ± 0.143 kg h−1. Penaeus semisulcatus emerged as the predominant species (mean CPUE: 3.77 ± 0.28 kg h−1), followed by Metapenaeus monoceros (mean CPUE: 0.1 ± 0.02 kg h−1). Significant differences in CPUE were observed among species, including P. semisulcatus, Penaeus hathor, and Penaeus pulchricaudatus, although CPUE differences between the two fishing grounds were minor, likely due to their proximity and similar environmental conditions. The bycatch analysis identified a total of 72 species across 28 families, with significant variation in the relative ratios. Sepiidae species constituted 31.8% of the total bycatch, followed by Portunidae species (24.8%). Discard patterns also varied, with Gerres oyena being the most commonly discarded species (mean discard ratio: 11.37% ± 1.89%), followed by Equulites klunzingeri (mean discard ratio: 8.76% ± 2.00%). While CPUE differences between Al Qunfudhah and Jizan were modest, this study highlights the need for expanded spatial and temporal coverage to enhance future analyses. These findings underscore the importance of integrated data for a comprehensive understanding of fishing effort and bycatch dynamics, supporting sustainable fisheries management in the Red Sea. By addressing bycatch and discard practices, this research contributes to efforts to mitigate ecological impacts and promote sustainable resource use in Saudi Arabia’s fisheries sector.