In 2020, a state of emergency was declared to control the devastating impact of coronavirus, leading to temporary school closures in Japan, meaning that school lunches were not provided to the majority of schoolchildren. Using questionnaires completed by participants’ guardians, we examined the relationship between household income and the quality of meals in Japanese schoolchildren before, during, and after the state of emergency. Participants (1111 children, 10–14 years old) were chosen to form a nationally representative sample of the Japanese population. “Well-balanced dietary intake” was defined as the intake of (i) meat, fish, or eggs and (ii) vegetables. The desired prevalence was defined as equal to or more than twice a day. Household income was divided into quartiles. “Well-balanced dietary intake” was lower in all households during the state of emergency compared with before. The proportion of those with a “well-balanced dietary intake” at least twice a day was notably low in both Q3 and Q4 during the state of emergency compared with before the declared state of emergency; relative risk increase (95% CI) were Q1: −19.0% (−19.6% to −18.4%), p < 0.001, Q2: −21.3% (−22.1% to −20.6%) p < 0.001, Q3: −25.4% (−26.1% to −24.7%), p < 0.001, and Q4: −34.8% (−35.6% to −34.0%), p < 0.001. The interaction p (vs. Q1) of Q2, Q3, and Q4 were all <0.001. Guardians from low-income households had significantly higher rates of having less: time, psychological room, and financial position to prepare meals during the state of emergency. Our results suggest that schoolchildren’s quality of meals worsened during the state of emergency, especially in low-income households, because school lunches were not provided.