Objectives The use of intrathecal fluorescein (ITF) has become an increasingly adopted practice for the identification of cerebrospinal fluid (CSF) leaks during endoscopic skull base surgery for pituitary adenomas. Administration through lumbar puncture can result in postoperative positional headaches, increasing morbidity, cost, and length of stay. We sought to identify the incidence of and variables associated with postoperative headaches to determine if there was a subgroup of patients in whom this procedure should be avoided. Methods We conducted a retrospective single-institution review of 148 patients who underwent endoscopic resection with ITF for pituitary adenoma between December 2003 and February 2016. We excluded patients who had lumbar drains and with intraoperative CSF leak, as these patients may have other headache etiologies. Patient demographics, comorbidities, tumor features, surgical approach, surgical closure, and histology were recorded. Primary outcomes included the presence of postoperative and positional headaches. Results We identified 62 patients with postoperative headaches (41.9%) and 10 with positional headaches (6.8%), of whom 6 underwent blood patch with complete resolution. Following univariate analysis, there was a significant positive association with prolactin-secreting tumors (p = 0.008). There was a negative association with a history of hypertension (p = 0.0001) and age (p = 0.01). Following multivariate modeling, the significance for hypertension (p = 0.01) was preserved. Conclusions Positional headaches in patients who receive ITF are uncommon and should not limit its use in the preparations for endoscopic resection of pituitary adenomas. Avoiding ITF in younger patients without hypertension with prolactinomas might decrease the risk of post-ITF positional headaches.