This paper attempts to identify the extent to which the affective characteristics of Malaysian and Singaporean students’ attainment compared to the OECD average in Programme for International Student Assessment (PISA) 2012, and examine the influence of students’ affective characteristics, gender, and their socioeconomic status on mathematics performance at both student and school levels. Sample consisted of 5197 and 5546 15-year-old Malaysian and Singaporean students. Data were analysed using hierarchical linear modelling approach with HLM 7.0 software. Results showed that the Index of economic, social, and cultural status (ESCS), mathematics self-efficacy, and mathematics anxiety have significant effects on mathematics performance in Malaysia and Singapore at the student level. Proportion of boys at the school level has no significant effects on mathematics performance for both Malaysian and Singaporean students. ESCS mean at the school level has positive and significant effects on mathematics performance in Malaysia, but not in Singapore. Limitations, implications, and future studies were discussed.