This study aims to explore the impact of fructooligosaccharides (FOS) on physicochemical, rheological, and microbiological properties of lactose‐free functional yogurts fermented with probiotic cultures. Milk was hydrolyzed by addition of β‐galactosidase and supplemented with FOS at 3% (wt/wt). Lactose hydrolysis and FOS supplementation increased acidification rate during fermentation of yogurts. FOS helped to improve syneresis but resulted in weaker gel network. Viability of lactic acid bacteria increased when FOS was added. The results suggest that it is possible to obtain a lactose‐free yogurt with functional properties contributing in improved nutritional characteristics suitable for people with lactose intolerance. Practical applications Lactose intolerance affects more than 75% of world population. This lactase deficiency condition limits people from consuming healthy dairy products. Although yogurts are known to have reduced lactose content, their lactose content, in fact, is still high. Manufacturing of low lactose and lactose‐free milk has been developed. However, the variety of products is limited. In this present study, development of lactose‐free yogurts enhanced with fructooligosaccharides as prebiotics was studied. Physicochemical, rheological, and microbiological characteristics of yogurts were evaluated. We believe that dairy product manufacturers can benefit from our findings and utilize our approach to create a new functional product for people with lactose intolerance.