Objective: To investigate the application of fine needle aspiration cytology (FNAC) in the diagnosis of malignant tumors on children’s body surface. Methods: Combined with clinical and histopathological data, the cytological diagnosis and cytological characteristics of suspected malignant tumors in children (0–16 years old) from January 2014 to November 2017 were analyzed retrospectively. Results: A total of 16 cases of malignant tumor and suspected malignant tumor in children were diagnosed by needle aspiration cytology. There were 3 cases of lymphoma, 3 cases of papillary thyroid carcinoma, 1 case of highly differentiated follicular carcinoma, 1 case of thyroid carcinoma metastasis, 3 cases of nasopharyngeal carcinoma metastasis, 1 case of fibro sarcoma, 1 case of rhabdomyosarcoma, 1 case of spindle cell sarcoma, 1 case of Langerhans cell histiocytosis. In this group, there was a false positive result, that is, FNAC was diagnosed as suspicious malignant tumor cells, while the histopathological results were yellow granuloma. One case of malignant tumor was misdiagnosed as Hodgkin's lymphoma by FNAC and histopathology confirmed as nasopharyngeal metastatic carcinoma. The results of the other 14 cases were consistent with histopathological results. The accuracy of FNAC in diagnosis of superficial suspicious malignant tumor in children was 87.5%. Conclusion: FNAC is an effective method for preoperative screening of malignant tumors in children.