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Ferredoxin:NADP-oxidoreductase (FNR) catalyzes the reversible exchange of electrons between ferredoxin (Fd) and NADP(H). Reduction of NADP+ by Fd via FNR is essential in the terminal steps of photosynthetic electron transfer, as light-activated electron flow produces NADPH for CO2 assimilation. FNR also catalyzes the reverse reaction in photosynthetic organisms, transferring electrons from NADPH to Fd, which is important in cyanobacteria for respiration and cyclic electron flow (CEF). The cyanobacterium Synechocystis sp. PCC6803 possesses two isoforms of FNR, a large form attached to the phycobilisome (FNRL) and a small form that is soluble (FNRS). While both isoforms are capable of NADPH oxidation or NADP+ reduction, FNRL is most abundant during typical growth conditions, whereas FNRS accumulates under stressful conditions that require enhanced CEF. Because CEF-driven proton pumping in the light–dark transition is due to NDH-1 complex activity and they are powered by reduced Fd, CEF-driven proton pumping and the redox state of the PQ and NADP(H) pools were investigated in mutants possessing either FNRL or FNRS. We found that the FNRS isoform facilitates proton pumping in the dark–light transition, contributing more to CEF than FNRL. FNRL is capable of providing reducing power for CEF-driven proton pumping, but only after an adaptation period to illumination. The results support that FNRS is indeed associated with increased cyclic electron flow and proton pumping, which is consistent with the idea that stress conditions create a higher demand for ATP relative to NADPH.