Introduction: Pulmonary spindle cell and mesenchymal lesions are paradox for pathologists due to their rarity, overlapping morphology, and differentials ranging from benign to malignant lesions, and correct diagnosis is essential due to major treatment implications. This study highlights the role of fine-needle aspiration cytology, clot core biopsy, and immunohistochemistry in diagnosis of spindle cell lesions in lung, thus playing a key role in patient management. Methods: It is a retrospective study of lung FNA with predominantly spindle and mesenchymal cells from 2015–2020 which were classified cytomorphologically into spindle, epithelioid, small round cell, and biphasic, and IHC panels are applied accordingly. FNA from mediastinum and chest wall was excluded. Results: 60 cases of lung FNA with spindle and mesenchymal cells were identified and included 6 benign and 54 malignancies which included 24 primary pulmonary malignancies and 30 metastases. Most common primary malignancy was sarcomatoid carcinoma, and most common metastasis was malignant peripheral nerve sheath tumour. FNA was paucicellular in 7 cases and was reported as benign in 7 cases and malignant in 46 cases. There were two false-negative cases. One case of pulmonary blastoma was reported as inflammatory pseudotumour on cytology, and other case of chondrosarcoma was reported as chondroid tumour. Sensitivity and specificity of FNA in distinguishing benign lesions and malignancies were 93.8% and 100%, respectively. Conclusion: FNA along with clot core biopsy/cell block and IHC plays a pivotal role in the subsequent pathway taken for diagnostic or therapeutic management of these patients without the need for second sampling or trucut biopsies in a low resource setting.