The upper endoscopy procedure takes only about 15-30 minutes. The colonoscopy procedure takes about 30-45 minutes on average.Because time before your endoscopy and a period of recovery, you and your escort should expect to spend 90-120 minutes at our facility.he upper endoscopy procedure takes only about 15-30 minutes. The colonoscopy procedure takes about 30-45 minutes on average.Because time before your endoscopy and a period of recovery, you and your escort should expect to spend 90-120 minutes at our facility.