This cross-sectional study aimed to assess the relationship between self-perceived food literacy (SPFL) and quality of overall diet and main meals in Japanese adults. In total, 5998 adults aged 20–79 years were included in this analysis. The SPFL was assessed using the Japanese version of the 29-item Dutch SPFL scale (score range 1–5). Using validated dietary information, the Healthy Eating Index-2015 (HEI-2015) was calculated (score range 0–100). The mean SPFL was 3.18; the internal consistency of the overall scale was considered good (Cronbach's alpha: 0.80). The mean HEI-2015 for overall diet was 50.4. The SPFL was significantly and positively associated with the HEI-2015. Using multiple linear regression, one point increase of SPFL corresponded to an increase in HEI-2015 by a point of 4.8 for overall diet, 6.2 for breakfast, 4.6 for lunch, and 3.6 for dinner (all P < 0.0001). Six of the eight domains of SPFL (i.e., food preparation skills, resilience and resistance, healthy snack styles, examining food labels, healthy budgeting, and healthy food stockpiling) were significantly associated with the HEI-2015 for overall diet. When the HEI-2015 for each meal was examined, the domains showing significant associations with all three meals included food preparation skills, healthy snack styles, and healthy budgeting. The healthy food stockpiling was associated with the HEI-2015 for breakfast and lunch, but not dinner. The social and conscious eating and daily food planning were associated with the breakfast HEI-2015 only, with the resilience and resistance associated with the dinner HEI-2015 only. In conclusion, the SPFL was cross-sectionally associated with the quality of overall diet and main meals in Japanese adults. Further observation and intervention studies are needed to confirm the associations observed here.