Abstract This paper proposes a new synchronization scheme called compound-combination synchronization. The scheme is investigated using six chaotic Josephson junctions evolving from different initial conditions based on the drive-response configuration via the active backstepping technique. The technique is applied to achieve compound-combination synchronization of: (i) six identical third order resistive-capacitive-inductive-shunted Josepshon junctions (RCLSJJs) (with three as drive and three as response systems); (ii) three third order RCLSJJs (as drive systems) and three second order resistive-capacitive-shunted Josepshon junctions (RCSJJs (as response systems). In each case, sufficient conditions for global asymptotic stability for compound-combination synchronization to any desired scaling factors are achieved. Numerical simulations are employed to verify the feasibility and effectiveness of the compound-combination synchronization scheme. The result shows that this scheme could be used to vary the junction signal to any desired level and also give a better insight into synchronization in biological systems wherein different organs of different dynamical structures and orders are involved. The scheme could also provide high security in information transmission due to the complexity of its dynamical formulation.