Follicle count, a pivotal metric in the adjunct diagnosis of polycystic ovary syndrome (PCOS), is often underestimated when assessed via transvaginal ultrasonography compared to MRI. Nevertheless, the repeatability of follicle counting using traditional MR images is still compromised by motion artifacts or inadequate spatial resolution. In this prospective study involving 22 PCOS patients, we employed periodically rotated overlapping parallel lines with enhanced reconstruction (PROPELLER) and single-shot fast spin-echo (SSFSE) T2-weighted sequences to suppress motion artifacts in high-resolution ovarian MRI. Additionally, deep learning (DL) reconstruction was utilized to compensate noise in SSFSE imaging. We compared the performance of DL reconstruction SSFSE (SSFSE-DL) images with conventional reconstruction SSFSE (SSFSE-C) and PROPELLER images in follicle detection, employing qualitative indices (blurring artifacts, subjective noise, and conspicuity of follicles) and the repeatability of follicle number per ovary (FNPO) assessment. Despite similar subjective noise between SSFSE-DL and PROPELLER as assessed by one observer, SSFSE-DL images outperformed SSFSE-C and PROPELLER images across all three qualitative indices, resulting in enhanced repeatability in FNPO assessment. These results highlighted the potential of DL reconstruction high-resolution SSFSE imaging as a more dependable method for identifying polycystic ovary, thus facilitating more accurate diagnosis of PCOS in future clinical practices.