The electronic-structure and magnetic properties of hydrogenated silicon nanocrystals doped with pairs of manganese atoms are investigated using spin-density-functional theory. Formation energies and total magnetic moments sensitively depend on the two sites occupied by manganese. Usually pairs at interstitial and substitutional sites with small total moment are energetically favored. Pairs at sites with the same character tend to ferromagnetic spin arrangements which are, however, significantly influenced by their noncollinearity. The resulting magnetic ordering is clearly related to the impurity levels and their occupation. The magnetic coupling is distance dependent, antiferromagnetic for small distances, and almost ferromagnetic for larger Mn-Mn distances. A Rudderman-Kittel-Kasuya-Yoshida-type exchange mechanism may describe the distance dependence but simultaneously not its magnitude.