Background: Intracytoplasmic lumina (ICL) are observed in several cancers, including urothelial carcinoma (UC). We have reported that ICL in urine cytology (cICL) is more frequent in high-grade UCs than in low-grade UCs; however, the correlation between the presence of ICL and prognosis is unclear. Objectives: The aim of this work was to determine the association between cICL and prognosis in bladder cancer. Method: We retrospectively investigated 87 patients with bladder cancer who received a histological diagnosis within 3 months of urine cytology at Kanazawa Medical University between 2003 and 2007. The cytological diagnosis and the number of cICL, histological diagnosis, tumor grade or variant, pT stage, ICL in histological specimens, and immunohistochemistry for mucins were evaluated. Data on the treatment type, recurrence, survival, cause of death, and length of follow-up were collected from electronic medical records. Results: Muscle invasion, high-grade UC, lymph node metastasis, distant metastasis, adjuvant therapy, and disease-related mortality were more frequent in patients with cICL-positive bladder cancer than in those without cICL-positive bladder cancer. Immunohistochemistry revealed the expression of Muc-1 and Muc-4 in patients with cICL-positive bladder cancer. Univariate analysis revealed that cytological diagnosis by the Paris system and the 2015 version of the Japanese reporting system, muscle invasion, high-grade UC, lymph node metastasis, distant metastasis, and adjuvant chemotherapy and/or radiotherapy were significant factors associated with prognosis. Furthermore, survival was shorter in patients with cICL-positive non-muscle-invasive bladder cancer than in those with cICL-negative non-muscle-invasive bladder cancer. In the multivariate analysis, only distant metastasis was significantly associated with survival. Conclusions: cICL predicted shorter survival in patients with non-muscle-invasive bladder cancer, suggesting that ICL is one of the important diagnostic features of high-grade UC with a worse prognosis in urine cytology.