Bladder pain syndrome/Interstitial cystitis (BPS/IC) is clinically of diverse types because different causes contribute to the development of their symptoms. It is important to classify patients into various groups based on the possible etiopathogenesis of their condition. Treatment may be tailored to each specific group according to the possible cause. Twenty-five patients diagnosed with BPS/IC were categorized into four different clinical phenotypes (CP) based on their history of symptoms, allergy, dysfunctional voiding, neuropathic pain, and the presence of Hunner's ulcer. Some patients could be classified into multiple groups. The patients were given oral pentosan polysulfate, and treatment specific to their CP. Patients in CP1, CP2, and CP3 groups received, respectively hydroxyzine, clonazepam, and amitriptyline. Patients with Hunner's lesions (HL) (CP4) underwent hydro distension and ablation of the lesion, followed by intravesical instillation of heparin and hydrocortisone. The patients were evaluated using the Apollo clinical scoring (ACS) system and their clinical scores were recorded at 1, 3, and 6 month(s). Among the 25 patients, 5, 7, 4, and 9 patients were classified into CP 1 - CP4 groups respectively, and were all subjected to ACS assessment. In CP1 group (allergy group), 80% (4/5) of patients responded well to the treatment and 20% (1/5) had unsatisfactory responses. In CP2 group (dysfunctional voiding group), 71.42% (5/7) patients had good, and 28.57% (2/7) had excellent responses. In CP3 group (neuropathic pain group), 28.57% (3/4) patients had excellent, and 75% (1/4) patients had good responses. In CP4 group (HL group), 33.33% (3/9) patients had unsatisfactory, 44.44% (4/9) achieved good, and 22.22% (2/9) had excellent responses. Overall, 16% (4/25) patients had unsatisfactory, 56% (14/25) attained good, and 28% (7/25) had an excellent response at the completion of the study. Using clinical phenotyping-based features indicative of etiology could potentially improve treatment outcomes by targeting the specific pathological processes contributing to the patients' symptoms.