Background Preoperative mediastinal staging is crucial for the optimal management of clinical stage I non-small cell lung cancer (NSCLC). Purpose To develop a deep learning signature for N2 metastasis prediction and prognosis stratification in clinical stage I NSCLC. Materials and Methods In this retrospective study conducted from May 2020 to October 2020 in a population with clinical stage I NSCLC, an internal cohort was adopted to establish a deep learning signature. Subsequently, the predictive efficacy and biologic basis of the proposed signature were investigated in an external cohort. A multicenter diagnostic trial (registration number: ChiCTR2000041310) was also performed to evaluate its clinical utility. Finally, on the basis of the N2 risk scores, the instructive significance of the signature in prognostic stratification was explored. The diagnostic efficiency was quantified with the area under the receiver operating characteristic curve (AUC), and the survival outcomes were assessed using the Cox proportional hazards model. Results A total of 3096 patients (mean age ± standard deviation, 60 years ± 9; 1703 men) were included in the study. The proposed signature achieved AUCs of 0.82, 0.81, and 0.81 in an internal test set (n = 266), external test cohort (n = 133), and prospective test cohort (n = 300), respectively. In addition, higher deep learning scores were associated with a lower frequency of EGFR mutation (P = .04), higher rate of ALK fusion (P = .02), and more activation of pathways of tumor proliferation (P < .001). Furthermore, in the internal test set and external cohort, higher deep learning scores were predictive of poorer overall survival (adjusted hazard ratio, 2.9; 95% CI: 1.2, 6.9; P = .02) and recurrence-free survival (adjusted hazard ratio, 3.2; 95% CI: 1.4, 7.4; P = .007). Conclusion The deep learning signature could accurately predict N2 disease and stratify prognosis in clinical stage I non-small cell lung cancer. © RSNA, 2021 Online supplemental material is available for this article. See also the editorial by Park and Lee in this issue.