This paper summarizes outcomes of a single-center study of intracavitary brachytherapy (IBT) with stereotactically applied phosphorus-32 ((32)P) colloid for treatment of cystic craniopharyngiomas. We assessed its efficacy and safety, on the basis of clinical and radiological outcomes in one of the largest reported patient series. Between 1992 and 2011, 53 patients were treated with IBT, 14 without previous treatment and 39 who had previously been treated for recurrent cysts. Intervention was performed by applying 200 Gy to the internal cyst wall (median volume 6.1 ml). Median clinical and radiological follow-up were 60.2 and 53.0 months, respectively. Actuarial tumor cyst control was 86.0 ± 5.3 % at 12, 24, and 60 months. Actuarial out-of-field control (development of new cysts or progression of solid tumor parts) was 90.9 ± 4.3, 84.0 ± 5.6, and 54.5 ± 8.8 % after 12, 24, and 60 months, respectively. Corresponding actuarial overall progression-free survival was 79.4 ± 6.1, 72.4 ± 6.8, and 45.6 ± 8.7 % at 12, 24, and 60 months, respectively. Visual function improved for 12 patients (23.5 %), remained unchanged for 34 patients (66.7 %), and worsened for five patients (9.8 %), correlating with tumor progression in each case. Endocrinological deterioration occurred for ten patients (19.6 %); for nine patients this was a result of tumor progression or after tumor resection and for one it was attributed to irradiation. Within six months of IBT seven patients (13.7 %) experienced transient neurological deficits and two patients (3.9 %) deteriorated permanently (hemiparesis and third nerve palsy). Stereotactically applied (32)P is highly efficacious for control of cystic components of craniopharyngiomas and is associated with a low risk of permanent morbidity. The procedure does not, however affect the development of new cysts or the progression of solid tumor parts.