This paper assesses the clinical and imaging characteristics, histopathological findings, and treatment outcomes of patients with Rathke's cleft cyst (RCC), as well as identifies potential risk factors for preoperative visual and pituitary dysfunction, intraoperative cerebrospinal fluid (CSF) leak, and recurrence. Through analyzing these factors, the study aims to contribute to the current understanding of the management of RCCs and identify opportunities for improving patient outcomes. We performed a retrospective analysis of 45 RCC patients between ages 18-80 treated by Endoscopic Endonasal Approach (EEA) and cyst marsupialization between 2010 and 2022 at a single institution. The median patient age was 34, and 73% were female. The mean follow-up was 70 ± 43 months. Preoperative visual impairment correlated with cyst diameter (OR = 1.41, 95% CI = 1.07 to 1.85, p-value = 0.01) and older age (OR = 1.06, 95% CI = 1.01 to 1.11, p-value = 0.02). Intraoperative CSF leaks were 11 times more likely for cysts ≥ 2cm (OR = 11.3, 95% CI = 1.25 to 97.37, p-value = 0.03), with the odds of leakage doubling for every 0.1cm increase in cyst size (OR = 1.41, 95% CI = 1.08 to 1.84, p-value = 0.01). Preoperative RCC appearing hypointense on T1 images demonstrated significantly higher CSF leak rates than hyperintense lesions (OR = 122.88, 95% CI = 1.5 to 10077.54, p-value = 0.03). Preoperative pituitary hypofunction was significantly more likely in patients with the presence of inflammation on histopathology (OR = 20.53, 95% CI = 2.20 to 191.45, p-value = 0.008 ) and T2 hyperintensity on magnetic resonance imaging (MRI) sequences (OR = 23.2, 95% CI = 2.56 to 211.02, p-value = 0.005). Notably, except for the hyperprolactinemia, no postoperative improvement was observed in pituitary function. Carefully considering risk factors, surgeons can appropriately counsel patients and deliver expectations for complications and long-term results. In contrast to preoperative visual impairment, preoperative pituitary dysfunction was found to have the least improvement post-surgery. It was the most significant permanent complication, with our data indicating the link to the cyst signal intensity on T2 MR and inflammation on histopathology. Earlier surgical intervention might improve the preservation of pituitary function.