Pseudomonas aeruginosa is an organism commonly found in the environment and one of the most common causes of human urinary tract infections in developed and developing countries. The present study aimed to investigate the effect of five medicinal plant extracts on the isolated drug‐resistant P. aeruginosa clinical isolates. A total of 100 urine samples were collected from Nagaa Hammadi and Qena General Hospitals and private medical analysis laboratories in Qena governorate, Upper Egypt. Samples were screened for the prevalence of UTI pathogens by biochemical tests, antibiotics sensitivity, detection of virulence, and antibiotic‐resistant genes by using multiplex PCR. P. aeruginosa is by far the subdominant causative agent with a percentage of 14%. Clinical isolates were multidrug‐resistant, containing bla_TEM, bla_SHV, toxA, lasB, pslA, and fliC resistant and virulence genes. Based on bioactivity, the ethanolic extract of clove (Syzygium aromaticum) was the most active extract among tested medicinal plants and had the maximum zone of inhibition sized 23 mm against tested bacteria. The results of the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) showed a high decrease of inhibition within a concentration range of (10 to 121.25 mg/mL and 20 to 30 mg/mL, respectively). Further, major compounds of oleic acid (27.22%), guanosine (8.91%), indole (6.83%), 1‐eicosene (6.30%), and cis‐10‐nonadecenoic acid (5.37%) were determined among 12 bioactive compounds in the ethanolic extract of S. aromaticum using gas chromatography‐mass spectrometry (GC‐MS). These results indicated that the ethanolic extract of S. aromaticum is a promising antibacterial agent for further studies aiming to control bacterial infections including MDR bacteria and develop novel therapeutic alternatives for the treatment of UTI.