Voiding dysfunction is a common disease among the elderly male population. However, few studies have elucidated the flow dynamics of the disease mechanism. We attempted to clarify the fluid dynamics of urine in the prostatic urethra (PU) in patients with bladder outlet obstruction (BOO), a common disease associated with voiding dysfunction. A model of normal PU and three phase models following the BOO progression were prepared using 3D CAD software tracing cystourethroscopic images. In fluid dynamics computation, the normal detrusor pressure was applied to the bladder side in each model. Results of fluid simulation were compared for flow trajectory line, fluid energy dynamics using Bernoulli's principle and pressure loss coefficient. In the BOO model, a large vortex was observed adjacent to the bladder outlet (BO) with increased hydraulic energy loss during the passage through the tract. In contrast, opening of the BO eliminated the vortex with reduction of hydraulic energy loss. These results corresponded with clinical data measured by catheterized pressure sensors inserted into the urethra, and those of urethral diameter measured by urethrography. Fluid dynamics simulation using CAD models can clarify the mechanism of voiding dysfunction in a less invasive and more acceptable way in patients with BOO.