Socioeconomic inequalities in eating habits have a profound impact on the health of adolescents. The aim of the present study was to evaluate socioeconomic disparities in the eating habits of Czech adolescents and to compare their change between 2002 and 2014. The data from the Czech Health Behavior in School-aged Children (HBSC) study conducted in 2002 and 2014 was utilized. The Family Affluence Scale (FAS) was used to assess socioeconomic disparities. Higher odds of daily consumption of fruit (2002: OR = 1.67; 2014: OR = 1.70, p < 0.001) and vegetables (2002: OR = 1.54; 2014: OR = 1.48, p < 0.001) were associated with high FAS in both genders. Adolescents with higher FAS were less likely to consume sweets (2002: OR = 0.72, p < 0.05) and more likely to eat breakfast on weekdays (2014: OR = 1.19, p < 0.05). In 2002 and 2014, the data showed lower odds of daily consumption of soft drinks (Low: OR = 0.47; Medium: OR = 0.43; High: OR = 0.41, p < 0.001), fruit (Low: OR = 0.73; Medium: OR = 0.74, p < 0.001; High: OR = 0.75, p < 0.05), sweets (Low: OR = 0.71; Medium: OR = 0.79, p < 0.001) and breakfast on weekends (High: OR = 0.70, p < 0.05), and a higher likelihood of eating breakfast on weekdays (Low: OR = 1.26, p < 0.01; Medium: OR = 1.13, p < 0.05). These findings play an important role in future public measures to improve dietary habits and decrease social inequalities in youth.