Introduction and hypothesis Interstitial cystitis/painful bladder syndrome (IC/PBS) is a chronic inflammatory condition of the submucosal and muscular layers of the bladder. So far, there is no effective and targeted treatment strategy for IC/ PBS. This study aimed to assess the efficacy and safety of intravesical instillation treatment in IC/PBS patients. Methods We searched various databases up to October 2015. A network meta-analysis was performed to compare global response assessment (GRA) for different treatment strategies, including botulinum toxin A (BoNTA), bacillus CalmetteGuerin (BCG), resiniferatoxin (RTX), lidocaine, chondroitin sulfate (CS), oxybutynin, and pentosan polysulfate (PPS). A traditional meta-analysis was also performed. Results Sixteen trials evaluating 905 patients were included. Network meta-analysis indicated that BoNTA had the highest probability of being the best treatment course according to GRA assessment results (probability 81.7 %). BCG or BoNTA therapy yielded significant improvement in GRA incidence according to traditional meta-analysis. Patients who received PPS showed higher urinary frequency results compared with the placebo groups. BCG-and PPS-treated patients had elevated urinary urgency treatment effects compared with placebo groups. Bladder capacity restoration results also showed significant improvements in patients who received BoNTA compared with placebo-treated individuals. Conclusions These findings indicate that BoNTA therapy has the highest probability of being the best therapy according to GRA, and significantly improves bladder capacity in IC/PBS patients. BCG treatment also significantly increases the incidence of GRA and improves the symptoms of urinary urgency. PPS can significantly improve urinary frequency and urgency symptoms in IC/PBS patients.