The therapeutic potential of methylene blue calls for the mathematical description of its effect on the restoration of mitochondrial function. The paper presents the mathematical model representing the functioning of the respiratory electron transport chain in mitochondria and the effect of methylene blue on the decrease in the number of free radicals, facilitating the return of the negatively charged electrons to the mitochondrial respiratory chain. Thus it contributes to the restoration of the energy potential of the cells in the metabolic diseases. The model makes it possible to calculate methylene blue dosages and the intervals between their administrations.