The study investigated DNA methylation patterns in urine samples from patients with non-muscle invasive bladder cancer (NMIBC) in Thailand. Five patients with high-grade NMIBC and three healthy volunteers were enrolled in this pilot study. Urine and blood samples were collected before surgical treatment. Analysis using sequencing identified 82 differentially methylated regions between NMIBC patients and controls, including 76 hypermethylated and 6 hypomethylated regions. Three genes—MIR124-3, IRX4, and LHX1-DT—showed the most significant hypermethylation. The method successfully distinguished NMIBC patients from healthy individuals. The findings suggest that DNA methylation in urine could serve as a non-invasive biomarker for diagnosis and monitoring of this cancer type.