High or variable ambient temperature can affect thermal regulation in livestock, but few studies have studied thermal variability during air and road transport, partly due to the lack of tools to compare thermal data from a long time series over periods of different duration. In this study, we recorded the ear skin temperature (EST) of 11 Duroc breeder pigs (7 females and 4 males) during commercial intercontinental transport from Canada to Spain, which included both road and aircraft travel and lasted 65 h. The EST was measured using a logger placed inside the left ear. Phase space diagrams EST, that is EST time series vs. itself delayed in time, were used to quantify the variability of the time-temperature series based on the areas that included all the points in the phase space. Phase space areas were significantly higher for all the animals during air travel, almost doubling that of road transport. Using the phase spaces, we identified an event during air transport that lasted 57 min, leading to a general decrease in EST by 8 °C, with respect to the average EST (34.1 °C). We also found that thermal variability was more stable in males (F = 20.81, p = 0.0014), which were also older and heavier.