Encouraging students' higher-order thinking skills (HOTs) has become an ultimate objective for several education programmes. Being a significant domain of scaffolding strategies, HOTs has been considered as a concern that should persistently be at the vanguard of reform agenda of science. The present research aims to examine the effect of scaffolding strategies on HOTs of middle school science students in the context of Saudi Arabia. To carry out the research aim, quasi-experimental design has been applied based on multiple-choice questions comprising 20 questions all distributed on four skills, namely, application, analysis, evaluation and creation. The total population of the research was 84 grade 9 students who all sat for both pre-test and post-test. Convenient sampling was chosen as a sampling method that typically suits both the experimental group (42 students) and the control group (42 students). After collection, data were analysed using both descriptive analysis, mean and standard deviation, and inferential statistics including t-test, one-way analysis of variance (ANOVA) and multivariate ANOVA. The effect of scaffolding strategies on the four skills was found to be significant (p <0.01). The present research can contribute to the enhancement of students' HOTs, provided that scaffolding strategies are applied in science classes and, from a research perspective, will be a reference for researchers who are interested in scaffolding strategies in the context of either Saudi Arabia or other countries.