Chronic bacterial prostatitis (CBP) is one of the most common relapsing urinary tract infection (UTI) in males. Catechin, an extract of green tea, is known to have anti-inflammatory and antimicrobial effects against various bacteria. However, catechin can be easily degenerated during digestion, and this may result in decreased absorption into the body. Nanocatechin is catechin coated with hydroxypropyl methyl cellulose by nanotechnology. It reduces degeneration during digestion and enhances absorption of catechin into the body. We evaluated the anti-inflammatory and antimicrobial effect of nanocatechin on CBP and also analyzed plasma concentration of catechins to evaluate absorptivity in an animal model. Forty rats demonstrating CBP were randomly divided into four groups: control, ciprofloxacin, catechin, and nanocatechin. After treatment, the results of microbiological culture of prostate and urine samples as well as histological findings of the prostate in each group were analyzed. Plasma concentration of catechins in catechin and nanocatechin groups was compared. The use of ciprofloxacin, catechin, and nanocatechin showed statistically significant decrease in bacterial growth and improvement in prostatic inflammation compared with the control group. The nanocatechin group showed statistically significant decrease in bacterial growth and improvement in prostatic inflammation compared with the catechin group. Plasma concentrations of epicatechin, gallocatechin gallate, and epigallocatechin gallate were significantly higher in the nanocatechin group than those in the catechin group. These results suggest that nanocatechin has better antimicrobial and anti-inflammatory effects on rat CBP than catechin due to higher absorption into the body.