We discover that the multiple degrees of freedom associated with magnetic skyrmions: size, position, and helicity, can all be used to control the Josephson effect and 0-π transitions occurring in superconductor/magnetic skyrmion/superconductor junctions. In the presence of two skyrmions, the Josephson effect depends strongly on their relative helicity and leads to the possibility of a helicity-transistor effect for the supercurrent where the critical current is changed by several orders of magnitude simply by reversing the helicity of a magnetic skyrmion. Moreover, we demonstrate that the Fraunhofer pattern can show a local minimum at zero flux as a direct result of the skyrmion magnetic texture. These findings demonstrate the rich physics that emerges when combining topological magnetic objects with superconductors and could lead to new perspectives in superconducting spintronics. PACS numbers: 73.43.Nq, 72.25.Dc, The interplay between superconductivity and ferromagnetism in hybrid structures has received much attention in recent years 1,2 , due to its allure from a fundamental physics viewpoint and also because of improved and new functionality brought about by using superconductors in spintronics 3 . Due to the proximity effect, the Cooper pairs induced in the ferromagnet acquire a finite center of mass momentum. Therefore, the pair amplitude oscillates in space which may result in a sign change of the Josephson current in ferromagnetic Josephson junctions. This effect can be used to control the quantum ground state of the system, altering from a state where the superconducting phase difference is 0 to a state where it is π 4-7 . This 0-π transition was originally observed in Josephson junctions through weak ferromagnets. 8,9 Also, in the presence of inhomogeneity of the magnetic order, triplet pairing with spin aligned with the local exchange field is generated in the ferromagnet due to spin flip scattering 10,11 . Experiments have successfully demonstrated the presence of such spin-triplet pairing by observing a Josephson current through strong ferromagnets [12][13][14] , which can be explained via the concepts of spin-mixing and spinrotation taking place near the superconductor/ferromagnet interface 15 . Using equal spin triplet pairings, the possibility arises to enhance existing effects or discover new ones in spintronics 3,[16][17][18][19][20] . Recently, it has been also proposed that inhomogeneous ferromagnet/superconductor junctions can create topological superconductivity. [21][22][23] Currently, much interest is garnered by magnetic skyrmions in chiral magnets [24][25][26] . Such objects are characterized by a topologically protected spin configuration. Due to their peculiar magnetic structure, several intriguing phenomena have been discovered such as topological and skyrmion Hall effects 27-29 and current-driven motion of skyrmion with ultralow current density [30][31][32][33][34] . It has been shown that magnetic skyrmions can be also driven by a temperature gradient [35][36][37][38] . A thermal ...