The population in the Western Pacific region is aging rapidly. Nutritional deficiency is prevalent in older adults; however, information regarding nutritional deficiency in this population is scarce. Using the 2019 Global Burden of Disease (GBD) results, the age-standardized disability-adjusted life years (DALYs) and years of healthy life lost due to disability (YLDs) from nutritional deficiency were estimated between 1990 and 2019 for this population. Average annual percentage change (AAPC) was used to assess temporal trends, and linear mixed-effects models were used to examine socioeconomic and sex inequalities. From 1990 to 2019, the age-standardized DALYs of nutritional deficiency in this population decreased from 697.95 to 290.95 per 100,000, and their age-standardized YLDs decreased from 459.03 to 195.65 per 100,000, with the greatest declines seen in South Korea (AAPCs < −5.0). Tonga had the least decline in DALYs (AAPC = −0.8), whereas Fiji experienced an increase in YLDs (AAPC = 0.1). Being female and having a lower sociodemographic index score was significantly associated with higher age-standardized DALYs and YLDs. The magnitude and temporal trends of the nutritional deficiency burden among older adults varied across countries and sex in the region, indicating that health policies on nutritional deficiency among older adults must be crafted to local conditions.