Background: We aimed to assess the effect of intrathecal morphine on postoperative pain after thoracoscopy. Methods: This double-blind randomized controlled trial was done on patients’ candidate for thoracoscopy referring to Afzalipour and Shahid Bahonar Hospitals in Kerman, Iran, 2015. 60 patients were divided into equal intervention and control groups. The intevention group received intrathecal morphine with a dose of 3-5 micrograms/kg/BW using a 23G spinal needle between the L3-L4. Control group received intravenous morphine with a dose of 0.1 mg/kg/BW. Their vital signs were monitored and upon gaining their conciousness and discharge from recovery, their pain severity was measured. Pain severity was assessed using the Visual Analog Scale and scored from 0 (no pain) to 10 (highest perceived pain). Data were analyzed using SPSS software. Independent t, paired t, and repeated-measure analysis of variance tests were sued as appropriated. Results: The mean±SD age of the patients in the interventiona and control groups were 51.62±12.3 and 56±12.24 years. The male/female ration in the intervention and control groups were 17.13 and 21.9. The two groups did not differ significantly with respect to age and sex. Pain severity socres reduced signifcantly after discharge from the recovery room in intervention group compared with control group. No significant difference was found between the administration of intrathecal and intravenous morphine with resepct to mean arterial pressure, heart rate, hemorrhage, and need for pain relievers, during surgery and recovery. Conclusion: The intrathecal administration of morphine significantly reduces postoperative pain compared with intravenous method in patients undergoing thoracostomy.