On-the-fly dynamics simulations were carried out using spin-flip time dependent density functional theory (SF-TDDFT) to examine the photoisomerization and photocyclization mechanisms of cis-stilbene following excitation to the ππ* state. A state tracking method was devised to follow the target state among nearly degenerate electronic states during the dynamics simulations. The steepest descent path from the Franck–Condon structure of cis-stilbene in the ππ* state is shown to reach the S1-minimum of 4,4-dihydrophenanthrene (DHP) via a cis-stilbene-like structure (referred to as (S1)cis-min) on a very flat region of the S1-potential energy surface. From the dynamics simulations, the branching ratio of the photoisomerization is calculated as trans:DHP = 35:13, in very good agreement with the experimental data, trans:DHP = 35:10. The discrepancy between the steepest descent pathway and the significant trans-stilbene presence in the branching ratio observed experimentally and herein computationally is clarified from an analysis of geometrical features along the reaction pathway, as well as the low barrier of 0.1 eV for the pathway from (S1)cis-min to the twisted pyramidal structure on the S1-potential energy surface. It is concluded that ππ*-excited cis-stilbene propagates primarily toward the twisted structural region due to dynamic effects, with partial branching to the DHP structural region via the flat-surface region around (S1)cis-min.