Background: Primary pulmonary myxoid sarcoma (PPMS) is an extremely rare lung sarcoma that is characterized in most cases by recurrent balanced chromosomal translocation t(2;22)(q33;q12) leading to the oncogenic fusion gene EWSR1-CREB1. Case presentation: We report a case of PPMS with molecular confirmation using fluorescence in situ hybridization (FISH) and DNA sequencing in a 45-year-old female patient. Computer tomography (CT) scanning revealed a peripheral circumscribed solid mass of 2.1 × 2 cm in the right lung superior lobe. Histologically, the tumor cells ranged from stellate, polygonal to chondrocyte-like or physaliferous-like, forming reticular network of delicate lacelike cellular strands and cords in abundant myxoid stroma. The tumor cell immunophenotype was positive for vimentin, EMA and negative for CK-pan, TTF-1, CAM5.2, S-100, calponin, SMA, desmin, ALK, CD31 and CD34. Molecular analysis demonstrated EWSR1-CREB1 gene fusion in this tumor. During 38 months of follow-up, the patient was alive with no clinical or radiological evidence of recurrence or metastasis. Conclusion: PPMS is a rare low-grade sarcoma with distinct histological and genetic features. We add another case to the literature of this rare tumor and report for the first time occurrence of chondrocyte-like and physaliferous-like tumor cells in this tumor, thus enriching its morphologic and cytologic spectrum.