This article examines gender gaps in academic performance (grades in mathematics and reading) between boys and girls of ninth-grade elementary schools in the Czech Republic. Our analysis is based on 2003 data from the Programme for International Student Assessment, encompassing the academic performance and family background of ninth-grade pupils. Similar to research on other countries, we find that girls strongly outperform boys in grades in Czech language, but that this gender gap is not explained by measured ability in reading nor on family background or student attributes. We also find gender bias in mathematics grades, after controlling for measured ability and other factors. Girls are also substantially more likely than boys to apply to secondary grammar schools, as well as aspire to a college education, even after controlling for measured ability. We put forward a number of theoretical perspectives that shed light on the possible causes of these empirical findings.