Personal development involves both cognitive and affective factors. It is therefore important to take the emotions into account in teaching and learning science. Secondary education is a particularly relevant stage because it is then that subsequent life itineraries, including undergraduate studies, will be decided. Previous research has found emotions to be markedly negative in secondary education pupils learning Physics and Chemistry. It is therefore important to understand clearly the everyday reality of secondary school classrooms in order to eliminate this negative view, and thus improve their motivation in learning these subjects. The objective of the present study was to determine and analyse the emotions experienced by secondary education pupils in learning Physics and Chemistry. The sample consisted of 202 pupils (50.5% boys, 49.5% girls) of the 2nd, 3rd, and 4th years of Compulsory Secondary Education in two schools of the province of Badajoz (Spain) during the 2013/2014 school year. The pupils' ages ranged from 13 to 19 years, with the average being around 14-15 years old. The most striking result was that there were significant differences in the mean frequencies of the emotions experienced according to which year the pupil was in. In general, positive emotions decreased and negative emotions increased as the academic level rose. In particular, the pupils experienced such positive emotions as joy, confidence, happiness, tranquillity, enthusiasm, and surprise with less frequency from the 2nd to the 4th year. And they experienced such negative emotions as worry, shame, disgust, and anger with greater frequency from the 2nd to the 3rd year.