The purpose of this study is to determine the effects of STEM applications and mastery learning on academic achievements, inquiry learning skills perceptions, motivations, their attitude towards STEM applications and permanence of information of the secondary school students. The study group of this study, which has been carried out in three stages, i.e. pilot, orientation and implementation, is composed of the seventh grade students attending a secondary school affiliated to Mus Provincial Directorate of National Education in the 2015-2016 school year. By means of the assignment of equal probability, two of these grades were designated as the experimental group and one as the control group. The application in question was made based on a semi-experimental study. SPSS package program was utilized to analyze the quantitative data obtained from the study. As a result of the research, It is found that STEM applications and mastery learning have positive effects on students' motivation for academic achievement and motivation. Furthermore, STEM applications and mastery learning have also been found to have a positive effect on the permanence of the learned information. It has also been observed that STEM applications and mastery learning do not have a positive effect on the inquiry learning skills perceptions for STEM attitude and science. As a result of these findings, suggestions on STEM applications and mastery learning were made.