Healthcare costs are lower for adults who consume more vegetables; however, the association between healthcare costs and fruit and vegetable varieties is unclear. Our aim was to investigate the association between (i) baseline fruit and vegetable (F&V) varieties, and (ii) changes in F&V varieties over time with 15-year healthcare costs in an Australian Longitudinal Study on Women’s Health. The data for Survey 3 (n = 8833 women, aged 50–55 years) and Survey 7 (n = 6955, aged 62–67 years) of the 1946–1951 cohort were used. The F&V variety was assessed using the Fruit and Vegetable Variety (FAVVA) index calculated from the Cancer Council of Victoria’s Dietary Questionnaire for Epidemiological Studies food frequency questionnaire. The baseline FAVVA and change in FAVVA were analysed as continuous predictors of Medicare claims/costs by using multiple regression analyses. Healthy weight women made, on average, 4.3 (95% confidence interval (CI) 1.7–6.8) fewer claims for every 10-point-higher FAVVA. Healthy weight women with higher fruit varieties incurred fewer charges; however, this was reversed for women overweight/obese. Across the sample, for every 10-point increase in FAVVA over time, women made 4.3 (95% CI 1.9–6.8) fewer claims and incurred $309.1 (95% CI $129.3–488.8) less in charges over 15 years. A higher F&V variety is associated with a small reduction in healthcare claims for healthy weight women only. An increasing F&V variety over time is associated with lower healthcare costs.