The elliptic flow of muons from the decay of charm and bottom hadrons is measured in pp collisions at s=13 TeV using a data sample with an integrated luminosity of 150 pb-1 recorded by the ATLAS detector at the LHC. The muons from heavy-flavor decay are separated from light-hadron decay muons using momentum imbalance between the tracking and muon spectrometers. The heavy-flavor decay muons are further separated into those from charm decay and those from bottom decay using the distance-of-closest-approach to the collision vertex. The measurement is performed for muons in the transverse momentum range 4-7 GeV and pseudorapidity range |η|<2.4. A significant nonzero elliptic anisotropy coefficient v2 is observed for muons from charm decays, while the v2 value for muons from bottom decays is consistent with zero within uncertainties.