Previous research showed that children’s physical activity is positively related to executive functions, whilst screen time shows negative associations. However, it is unclear how school-based sitting time and transitions from sitting to standing relate to cognition. We investigated the relationship between class time sitting/stepping/sit-to-stand transitions and cognitive functions in Grade 1–2 children. Overall, 149 children (7.7 ± 0.6 years old, 54% boys) participated. Measures included class time sitting/stepping/sit-to-stand transitions and: (i) response inhibition (i.e., response time and accuracy); (ii) lapses of attention; (iii) working memory; and (iv) brain activity (cortical haemodynamic response). Linear mixed-models, adjusting for age, sex, and clustering at the classroom level, found that more sitting time was associated with higher lapses of attention ($β$ = 0.12, p < 0.05). Children who stepped more had quicker inhibition response time ($β$ = −0.95, p < 0.01); however, they were less accurate in their responses ($β$ = −0.30, p < 0.05) and this was also observed with sit-to-stand transitions ($β$ = −0.26, p < 0.05). No associations were found with brain activity. In conclusion, reducing and breaking up sitting may help keep children focused, but the evidence regarding response inhibition is unclear.