The Thumbs food classification system was developed to assist remote Australian communities to identify food healthiness. This study aimed to assess: (1) the Thumbs system’s alignment to two other food classification systems, the Health Star Rating (HSR) and the Northern Territory School Canteens Guidelines (NTSCG); (2) its accuracy in classifying ‘unhealthy’ (contributing to discretionary energy and added sugars) and ‘healthy’ products against HSR and NTSCG; (3) areas for optimisation. Food and beverage products sold between 05/2018 and 05/2019 in fifty-one remote stores were classified in each system. System alignment was assessed by cross-tabulating percentages of products, discretionary energy and added sugars sold assigned to the same healthiness levels across the systems. The system/s capturing the highest percentage of discretionary energy and added sugars sold in ‘unhealthy’ products and the lowest levels in ‘healthy’ products were considered the best performing. Cohen’sκwas used to assess agreement between the Thumbs system and the NTSCG for classifying products as healthy. The Thumbs system classified product healthiness in line with the HSR and NTSCG, with Cohen’sκshowing moderate agreement between the Thumbs system and the NTSCG (κ= 0·60). The Thumbs system captured the most discretionary energy sold (92·2 %) and added sugar sold (90·6 %) in unhealthy products and the least discretionary energy sold (0 %) in healthy products. Modifications to optimise the Thumbs system include aligning several food categories to the NTSCG criteria and addressing core/discretionary classification discrepancies of fruit juice/drinks. The Thumbs system offers a classification algorithm that could strengthen the HSR system.