Observed upper-tropospheric temperature over the tropics (TTUT) shows a slowdown in warming rate during 1997–2011 despite the continuous warming projected by coupled atmosphere–ocean general circulation models (AOGCMs). This observation–model discord is an underlying issue regarding the reliability of future climate projections based on AOGCMs. To investigate the slowdown, we conducted ensemble historical simulations using an atmospheric general circulation model (AGCM) forced by observed sea surface temperature both with and without anthropogenic influences. The historical AGCM run reproduced a muted TTUT change over the central Pacific (CP) found in multiple observations, while the multi-AOGCM mean did not. Recent tropical Pacific cooling, which is considered natural variability, contributes to the muted trend over the CP and the resultant slowdown of TTUT increase. The results of this study suggest that difficulties in simulating the recent “upper-tropospheric warming hiatus” do not indicate low reliability of AOGCM-based future climate projections.