Background: Kleibsiella pneumoniae in urinary tract infections (UTIs) have grown for years. Antibiotic-resistant microorganisms make infection control and treatment difficult for clinicians. Efflux pumps contribute to K. pneumoniae's multidrug resistance. Objective: This study aimed to test Phenylalanine-Arginine β-Naphthylamide (PAβN) and Berberine as antibacterial agents against multidrug-resistant bacteria (UTI K. pneumonia isolates). Subjects and Methods: Between December 2021 and April 2022, five Baghdad hospitals collected 260 urine samples from outpatients and inpatients with urinary tract infections, both genders, aged 15 to 72. Results: We isolated 76 of the cultures (65.5%) and employed selective media, biochemical assays, and the VITEK2 system to identify bacteria as K. pneumoniae. Using the disc diffusion technique, it was demonstrated that clinical isolates of K. pneumoniae were moderately resistant to the majority of drugs. K. pneumoniae isolates were extremely resistant to Amoxicillin (96.1%), Trimethoprim (80.3%), Gentamicin, Amikacin and Meropenem (55.1%), and Ciprofloxacin (53.9%). The efflux pump inhibitor (PAβN) greatly boosted strain susceptibility to Ciprofloxacin. PAβN lowered MICs by 4–64-fold. The minimum inhibitory concentrations (MICs) of Berberine against ten multidrug-resistant K. pneumoniae isolates ranged from 3.9 to 500 μg/ml, indicating that Berberine affects K. pneumoniae growth at very low doses. Conclusion: In this work, Berberine was found to be an efflux pump inhibitor (EPI) and antibacterial drug that could overcome bacterial resistance mechanisms.