Heat stress is major welfare concern during transport of pigs in tropical climates, which can also lead to direct production costs. This study evaluated the dynamics of heat zones through the load and their relationship with heat stress of weaner pigs during road transport in a tropical climate. Both environmental (e.g. temperature and relative humidity) and physiological (e.g. respiratory frequency and lactate) measures were recorded from four vehicle journeys (70 km distance, 216 weaner pigs within each trailer load) within Ceará, northeastern Brazil. Geostatistics and fluid dynamics simulation techniques were applied to understand the dynamics of heat zones and ventilation patterns the truckload. Statistics based on canonical discriminant analysis and ANOVA were performed to verify the relationship between heat zones and heat stress in pigs. The results showed that, during transport, the generation of heat zones occurred with different magnitudes along the load (P < 0.05), which was harmonized by the ventilation dynamics. There was a heat core with high energy content, in the front region of the lower deck (LD) of the trailer. In this zone, weaners pigs had higher rectal temperature (+1.8 °C temperature difference), respiratory frequency (LD = 94 ± 1.3 breaths/min; UD = 86 ± 1.3 breaths/min), and blood cortisol concentration (LD = 32.9 ± 0.8 ng/mL; UD = 30.18 ± 0.6 ng/mL) (all P < 0.05). Weaners pigs transported in the upper deck (UD) compartments had the highest skin temperature (LD = 38.13 ± 0.3 °C; UD = 38.9 ± 0.22 °C) and the highest mean values of blood lactate (LD = 65.5 ± 1.11 m/M; UD = 71.60 ± 1.19 m/M) and Creatine kinase (LD = 3891.23 ± 69U/L; UD = 4107.43 ± 62U/L) (P < 0.05). Weaners transported in compartments of the LD of trailer were more susceptible to heat stress, while weaners in the UD compartments were more susceptible to physical stress and muscle exhaustion. These results provide additional evidence of heat zones within trailer compartments and highlight the requirement for the planning of pig transport operations in tropical climates to mitigate risks of heat stress.