Introduction: Bladder pain syndrome is a debilitating chronic disease of unknown etiology; it has negative impact on the quality of life. Intravesical therapy used in a patient who is refractory to conservative management. Intratrigonal botulinum toxin is shown to inhibit not only the release of acetylcholine and nor epinephrine, but also that of nerve growth factor, ATP, substance P and calcitonin gene-related peptide from the urothelium and in the nerve fibres decrease detrussor overactivity, bladder sensation, and visceral pain. Chondroitin sulfate is other intravesical agent, it replenish the protective GAGs layer. Material and Method: This is prospective study of 44 patients full filling the inclusion criteria. It was conducted in ruby hall clinic between September 2018 to January 2020. Patients were evaluated by history, physical examination, blood and urine examination, ultrasonography of abdomen, uroflowmetry, bladder diary, ICSI, ICPI and VAS scale. Patients were randomized in two groups. Group 1 had received botulinum toxin-A intratrigonal 100 IU diluted in 10ml normal saline given stat. Group 2 had been treated with intravesical chondroitin sulphate 2% sterile solution in 20ml vials weekly for 6 weeks. Both the groups were followed at 6weeks, 3months and 6 months and assessed for urinary frequency, urgency suprapubic pain, mean voided volume, ICSI, ICPI and VAS score. Result: Intratrigonal Botulinum toxin therapy had significant better outcome over intravesical Chondroitin sulfate in terms of urinary frequency, urgency suprapubic pain episodes, mean voided volume, ICSI, ICPI and VAS score at the end of study. Conclusion: Intra-trigonal botulinum toxin 100IU is a viable treatment option for BPS patients refractory to conservative therapy, with acceptable fewer side effect profile. Intravesical chondroitin sulfate 20ml , 2% is another intravesical therapy which require frequent instillation and its outcome is inferior as compare to intra-trigonal botulinum toxin 100IU.