In this work, the analysis of electron and proton transport in chloroplasts of higher plants has been carried out on the basis of a mathematical model, which takes into account the pH-dependent regulation of electron transfer and thioredoxin-dependent activation of the Calvin–Benson cycle (CBC) enzymes and the ATP synthase. The impact of reduced thioredoxin on the kinetics of electron transport, pH changes in the intrathylakoid space and ATP production has been simulated. Comparison of the computed and experimental data on the kinetics of P700 photooxidation has shown that the consideration of thioredoxin-dependent activation of the CBC and the ATP synthase provides an adequate description of the multiphase kinetics of P 700 + induction. The dynamics of electron flow through PSI and the partitioning of electron fluxes on the acceptor site of PSI has been simulated. The model predicts that at the initial stage of the induction period the alternative pathways, cyclic electron transport around PSI and electron flow to O2 (the Mehler reaction), play a significant role in photosynthetic electron transport chain, but their contribution attenuates upon the activation of the CBC reactions.