Objective To evaluate the clinical efficacy, surgical timing, and therapeutic value of deworming with praziquantel in combination with thoracoscopic surgery for treatment of pediatric refractory paragonimiasis-induced encapsulated pleural effusions. Methods The medical records of 15 children with paragonimiasis-induced encapsulated pleural effusions who underwent surgical treatment in Public Health Clinical Center of Chengdu from January 2015 to January 2025 were retrospectively analyzed. All cases received initial treatment with praziquantel pre-surgery at a dose of 75 mg/(kg·d), divided into 3 oral doses, for 3 consecutive days as one course of treatment, with an interval of one month between each course. Then, routine single port thoracoscopic surgery was performed a group of thoracic surgeons. Postoperative antibiotics administration, deworming, and rehabilitation training were given, and follow-up re-examinations were performed at 1, 3, 6, and 12 months post-surgery. Results The 15 children included 11 males and 4 females, with a median age of 8.50 (5.46, 10.79) years, and all cases had a thoracic-pulmonary type of paragonimiasis, including 7 cases complicated by abdominal type, 3 cases complicated by pericardial type, one case complicated by cerebral type, and one case complicated by subcutaneous nodule type. There were 14 children tested positive for serum IgG antibodies against Paragonimus, and the other one case was definitively diagnosed with paragonimiasis by pleural pathology despite sero-negativity. Preoperative chest CT scans displayed encapsulated effusions with pleural thickening and adhesions among all children, and 2 to 6 courses of treatment with praziquantel were given. All cases successfully completed thoracoscopic surgery, and typical empyema and fibrous septa were observed during the operation. Charcot-Leyden crystals were found in postoperative pathological specimens from 15 children, including parasite fragments seen in 2 cases and parasite eggs in one case. Routine blood tests at one-month post-surgical follow-up revealed that the absolute value of peripheral blood eosinophils in decreased from 3.70 (1.32, 8.33) × 10⁹/L pre-surgery to 0.34 (0.23, 0.56) × 10⁹/L post-surgery among all 15 children (Z = -3.41, P < 0.01), and eosinophils percentage decreased from 33.00% (16.60%, 44.70%) pre-surgery to 4.20% (2.10%, 6.50%) post-surgery (Z = -3.19, P < 0.01). All symptoms were relieved, and imaging showed good lung recruitment and no serious complications. Conclusion Combined treatment of deworming and thoracoscopic surgery may effectively remove lesions, promote lung recruitment and remarkably reverse host eosinophilic inflammation among children with paragonimiasis-induced encapsulated pleural effusions and unsatisfactory efficacy of medical treatment.