Time-dependent CP asymmetries in the decay rates of the singly Cabibbo-suppressed decays D0→K−K+ and D0→π−π+ are measured in pp collision data corresponding to an integrated luminosity of 3.0 fb−1 collected by the LHCb experiment. The D0 mesons are produced in semileptonic b-hadron decays, where the charge of the accompanying muon is used to determine the initial state as D0 or D¯0. The asymmetries in effective lifetimes between D0 and D¯0 decays, which are sensitive to indirect CP violation, are determined to beAΓ(K−K+)=(−0.134±0.077+0.026−0.034)% ,AΓ(π−π+)=(−0.092±0.145+0.025−0.033)% ,where the first uncertainties are statistical and the second systematic. This result is in agreement with previous measurements and with the hypothesis of no indirect CP violation in D0 decays.