Ionospheric ion temperature Ti is an excellent approximation to neutral temperature Tn in the thermosphere, especially for altitudes below 300 km. This analysis of long‒term Ti trends in the F region over different local times is based on a database of incoherent scatter radar (ISR) observations spanning more than three solar cycles during 1968–2006 at Millstone Hill and represents an extended effort to a prior study focusing on noon‒time only. This study provides important information for understanding the difference between the ISR and other results. A gross average of the Ti trend at heights of Ti ∼ Tn (200–350 km) is ∼ −4 K/decade, a cooling trend close to the Tn estimation based on the satellite neutral density data. However, there exists considerable variability in the cooling: it is strong during the day and very weak during the night with a large apparent warming at low altitudes (200–350 km); it is strong at solar minimum for both daytime and nighttime. The strongest cooling for altitudes below 375 km occurs around 90–120 solar flux units of the 10.7 cm solar flux, not at the lowest solar flux. There appears more cooling toward high magnetic activity, but this dependency is very weak. No consistent and substantial seasonal dependency across different heights was found. We speculate that a fraction of the observed cooling trend may be contributed by a gradual shifting away from the sub‒auroral region at Millstone Hill, as part of the secular change in the Earth's magnetic field. In this 39 year long series of data record, two anomalous Ti drops were noticed, and we speculate on their connection to volcano eruptions in 1982 and 1991. Key Points Ti trend at altitudes of Ti~Tn close to ‐4K/decade as a gross daily average Large day‐night, solar min‐max, and minor magnetic activity dependencies Potential impacts from magnetic field secular changes