The anomalous variability of extreme cases of the tropical tropopause provides insight into the stratosphere‐troposphere exchange process crucial for understanding climate change. The present study analyses the extreme variability of the tropopause and its thermal structure over the tropics using GPS radio occultation data over the period 2006–2019. The extremely cold and warm tropopauses and extremely high and low tropopauses are identified based on the cold point tropopause temperature and height, respectively, when their values exceed two standard deviations with respect to their climatological means. The analyses revealed frequent occurrence of extreme cases of tropopause over the Atlantic Ocean compared to the Western Pacific Ocean. Individually, extremely warm and low cases occur more frequently over the subtropics, while extremely cold and high cases occur frequently over the deep tropics. These extreme cases pose different thermal structures bounded within the extremely low and high tropopauses throughout the tropics. The height difference between the extremely high and low tropopause cases is wider over the Atlantic Ocean and adjoining areas compared to the western Pacific Ocean. The temperature difference between the extremely warm and cold tropopause cases is higher in the Atlantic, Central Pacific, and Indonesian regions compared to the American, Indian Ocean, and western Pacific Ocean regions. The relationship between the El Niño Southern Oscillation (ENSO) phases and extreme tropopause cases is also investigated which reveals a higher occurrence of extremely high tropopause cases during the El Niño phase while low tropopause cases during the La Niña phase. Our analysis also revealed the thermal patterns of the extreme cases characterising colder and sharper tropopause over the convective regions compared to subsidence regions.