We theoretically study the effect of the motion and the merging of Dirac cones on the interlayer magnetoresistance in multilayer graphene-like systems. This merging, which can be induced by a uniaxial strain, gives rise in a monolayer Dirac electron system to a topological transition from a semi-metallic phase to an insulating phase whereby Dirac points disappear. Based on a universal Hamiltonian, proposed to describe the motion and the merging of Dirac points in two-dimensional Dirac electron crystals, we calculate the interlayer conductivity of a stack of deformed graphene-like layers using the Kubo formula in the quantum limit where only the contribution of the n = 0 Landau level is relevant. A crossover from a negative to a positive interlayer magnetoresistance is found to take place as the merging is approached. This sign change of the magnetoresistance can also result from a coupling between the Dirac valleys, which is enhanced as the magnetic field amplitude increases. Our results describe the behavior of the magnetotransport in the organic conductor α-(BEDT)2I3 and in a stack of deformed graphene-like systems. The latter can be simulated by optical lattices or microwave experiments in which the merging of Dirac cones can be observed.