Objectives To differentiate the primary small-cell lung cancer (SCLC) and non-small-cell lung cancer (NSCLC) for patients with brain metastases (BMs) based on a deep learning (DL) model using contrast-enhanced magnetic resonance imaging (MRI) T1 weighted (T1CE) images. Methods Out of 711 patients with BMs of lung cancer origin (SCLC 232, NSCLC 479), the MRI datasets of 192 patients (lesions' widths and heights > 30 pixels) with BMs from lung cancer (73 SCLC and 119 NSCLC) confirmed pathologically were enrolled, retrospectively. A typical convolutional neural network ResNet18 was applied for the automatic classification of BMs lesions from lung cancer based on T1CE images, with training and testing groups randomized per patient to eliminate learning bias. A 5-fold cross-validation was performed to evaluate the classification of the model. The receiver operating characteristic (ROC) curve, accuracy, precision, recall and f1 score were calculated. Results For a 5-fold cross-validation test, the DL model achieved AUCs of 0.8019 and 0.8024 for SCLC and NSCLC patients with BMs, respectively, and a mean overall accuracy of 0.7515 & PLUSMN;0.04. The DL model performed well in differentiating the primary SCLC and NSCLC with BMs. Conclusion The proposed DL model is feasible and effective in differentiating the pathological subtypes of SCLC and NSCLC causing BMs, which may be used as a new tool for oncologists to diagnose noninvasively BMs and guide therapy based on the imaging structure of tumors.