The solid oxide fuel cells (SOFCs) represent a promising technology for sustainable power generation from hydrogen rich fuels with high efficiency of energy conversion. However, only a limited number of papers address the problem of on-line maximisation of the efficiency of SOFC operation. Optimal operating conditions are normally chosen either based on experience or by using elaborated models, which are not easy to obtain. Moreover, the process changes over time due to degradation, hence the model-based performance optimisation requires on-line model update. To avoid these problems, a model-free approach is proposed. It is realised in the form of a two-tier control structure where the low-level controllers take over control of the auxiliary units around the fuel cells, while the supervisory controller (SC) controller optimises the operation point of the system. The low-level controllers are conventional feed-forward feed-back controllers, while optimisation on the higher level is solved by using the extremum seeking approach. The proposed control system is demonstrated on a simulated 10 kW SOFC system showing reliable convergence, relative rise of efficiency up to 2% and easy design and maintenance.