In this study, the temperature biases and the ability of the ERA-5 product to reproduce the LiDAR variability in the 30–80 km altitude range were evaluated for the period 2005–2020, both for the winter and the summer months. During winter, temperatures from the ERA-5 dataset were in good agreement with LiDAR observations up to 45 km, while in the mesosphere, almost 70% of the ERA-5 profiles were cooler than those from LiDAR, except around 65 km. During summer, negative biases of −3 K were observed up to the stratopause, while significant positive biases of more than +10 K were found in the mesosphere. For the winter months, the variability observed by LiDAR, even during sudden stratospheric warming (SSWs) events, was reproduced accurately by the model in the upper stratosphere, but not in the mesosphere. Surprisingly, the LiDAR variability mainly due to propagating gravity waves in the summertime was also not reproduced by ERA-5 in the whole middle atmosphere. The model uncertainty associated with this variability, evaluated afterward with a new method, grew as expected with altitude and was more significant in winter than summer. A principal component analysis of the fluctuations of the temperature differences between the LiDAR and ERA-5 was performed to investigate the vertical coupling between 30 km and 70 km. The three first vertical modes illustrated 76% and 78% of the fluctuations of the temperature difference profiles in summer and winter, respectively, confirming the connection between the studied layers. The leading modes of the summer (49%) and winter (42%) possessed an anti-correlation between the upper stratosphere and the mesosphere, where fluctuations increased (at least ±5 K at 65 km) for both seasons due to the coarse vertical resolution in the model. The other modes showed an agreement between the LiDAR and ERA-5 fluctuations in the upper stratosphere and had a wave-like structure mainly located in the mesosphere, confirming that the model either overlooked or simulated imprecisely the gravity waves, leading to mesospheric inversions. Finally, SSWs impacted the ERA-5 temperature (deviation of ±3 K) some days before and after its trigger around the stratopause.