Within three functionals (TD‐B3LYP, TD‐BHandHLYP, and TD‐CAM‐B3LYP) in combination with four basis sets (3‐21g, 6‐31g, 6‐31g(d), and cc‐pvdz), global switching (GS) trajectory surface hopping molecular dynamics has been performed for cis‐to‐trans azobenzene photoisomerization up to the S1(nπ*) excitation. Although all the combinations show artificial double‐cone structure of conical intersection between ground and first excited states, simulated quantum yields and lifetimes are in good agreement with one another; 0.6 (±5%) and 40.5 fs (±10%) by TD‐B3LYP, 0.5 (±10%) and 35.5 fs (±4%) by TD‐BHandHLYP, and 0.44 (±9%) and 35.2 fs (±10%) by TD‐CAM‐B3LYP. By analyzing distributions of excited‐state population decays, hopping spots, and typical trajectories with performance of 12 functional/basis set combinations, it has been concluded that functional dependence for given basis set is slightly more sensitive than basis set dependence for given functional. The present GS on‐the‐fly time‐dependent density functional theory (TDDFT) trajectory surface hopping simulation can provide practical benchmark guidelines for conical intersection driven excited‐state molecular dynamics simulation involving in large complex system within ordinary TDDFT framework. © 2019 Wiley Periodicals, Inc.