Computational thinking, a form of thinking and problem solving, is defined as a mental process for abstracting problems and formulating solutions. Computational thinking is considered to be an essential skill for everyone and has become the centre of attention in education settings. There is a limited number of tools to measure computational thinking skills by multiple-choice questions, and limited research on the relationship between computational thinking and other domains. The purpose of this research is to investigate the relationship between computational thinking performance, perception of computational thinking skills and school achievement of secondary school students. Computational thinking performance of secondary school students in Kazakhstan is measured by using a bespoke multiple-choice test, which focuses on the following elements of computational thinking: logical thinking, abstraction and generalisation. The perceptions of computational thinking skills are self-reported using a pre-existing questionnaire, which covers the following factors: creativity, algorithmic thinking, cooperation, critical thinking and problem solving. The General Knowledge Test results that contain scores for 14 different subjects are used as indicators of students’ school achievement, with further sub-scores for the science subjects, language subjects and humanities. The sample group of 775 grade eight students are drawn from 28 secondary schools across Kazakhstan. The validity and reliability of the multiple-choice questions are established by using Item Response Theory models. The item difficulty, discrimination and guessing coefficients are calculated; and the item characteristic curves for each question and test information functions for each quiz are obtained. As a result, the multiple-choice questions are concluded as a valid and reliable tool to measure the computational thinking performance of students. Multiple regression is used to examine the relationship between computational thinking performance, perception of computational thinking and school achievement sub-scores. The results of the data analysis show that science subjects, language subjects and perception of computational thinking skills are significant predictors for computational thinking performance, showing a moderate relationship between computational thinking performance and school achievement. However, no significant relationship is found between humanities subject scores and computational thinking performance. This study also adds to the literature for the studies that investigate the relationship between computational thinking skills and other variables. This research contributes to the development of validated tools to measure computational thinking performance by using multiple-choice questions. This study investigates the relationship between computational thinking performance and general school achievement of secondary school students, and its findings shed light on the measurement of children’s cognitive development. The findings can help in designing better curricula by adjusting subjects that enhance children’s higher-order thinking abilities. The findings obtained in this research also adds to the literature for the studies that investigate the relationship between computational thinking skills and other variables.