Food fortification is considered as an important strategy to address micronutrient malnutrition, which is a key challenge in most developing countries. In Kenya, the National Food Security and Nutrition Policy focus on pilot efforts on food fortification. However, lack of empirical information on consumers’ awareness and preferences for fortified foods remains the barrier to the uptake of fortified foods. This study assessed the consumers’ awareness and analyzed their preferences for fortified sugar. Awareness was assessed using binary logit model while the preferences were determined through a choice experiment survey and random parameter logit (RPL) model. The study used primary data from a random sample of 350 consumers in Nairobi County (a completely urban setup), and Kakamega County (a relatively rural setup). The study found that about 55% of the households were aware of fortified sugar and that awareness levels were statistically higher for urban consumers. Results from binary logit regression showed that age of consumers, purchasing from supermarket, reading newspaper, living in urban area as well as having a child below the age of five years, were the significant factors influencing consumers’ awareness of fortified sugar. The RPL results indicated heterogeneous and high preferences for fortified sugar attributes particularly, for rural consumers. Further, an analysis of compensating surplus (CS) showed that different consumer segments were willing to pay a premium ranging from 77% to 300% (above the average price of current conventional sugar) for fortified sugar, suggesting that there is high potential for sugar fortification in Kenya. These findings offer useful insights for the development of preference-based sugar fortification programmes in Kenya. Moreover, the results would guide formulation of policies against micronutrient malnutrition in Kenya and other developing countries, with similar conditions.