This research aimed to compare the equated scores by the methods based on classical test theory (CTT) and kernel equating, using covariates design (NEC) and anchor test design (NEAT). TIMSS 2019 science test scores equated by both Tucker, Levine true score, Levine observed score, equipercentile equating (pre-smoothing and post-smoothing) methods in CTT, and linear and equipercentile methods in kernel equating. Additionally, the covariates in NEC design were “home resources for learning,” “student confidence in science and mathematics,” “like learning science,” “instructional clarity in science lessons,” “math achievement,” “sex,” and “speaking the language of the test at home”. The equating results in NEC were compared with those in NEAT and EG. The participants comprised 1699 4th-grade students who attended the e-TIMSS 2019 in Canada, Singapore, and Chile. Results were analyzed according to equating errors and differences between equated scores. The research concluded that math achievement and home resources for learning could be used as covariates in NEC to equate the science test in case equating could not be done in the NEAT. However, when the other variables were used as covariates in NEC, the equated scores were very similar to the EG. Also, Tucker (CTT) and post-stratification (kernel) yielded similar equated scores in linear equating, and these methods were similarly different from kernel linear equating in EG. In equipercentile equating, the equated scores obtained from the post-smoothing (CTT) and EG were close to each other but slightly differed from post-stratification.