Physical inactivity has emerged as an important and risk factor for cardiovascular and metabolic diseases, independent of levels of exercise engagement. Moreover, inactivity is associated with poor brain functioning. However, little data on the effects of physical inactivity on the brain is available and few methods are suitable to investigate this matter. We tested whether preventing lid climbing and reducing cage size could be used to model physical inactivity in mice. Sixty young adult C57Bl6 mice (10 weeks old) were divided over six groups with different housing conditions: in cages of three different sizes with lids that either allowed or prevented lid climbing. Housing under these conditions was maintained for a period of 19 weeks before the mice were killed for body composition analysis. Physical fitness tests performed around 5 and 10 weeks into the intervention revealed that motor coordination in the balance beam test was reduced by 30.65%, grip strength by 8.91% and muscle stamina in the inverted screen test by 70.37% in non-climbing mice as compared to climbing controls. Preventing climbing increased visceral fat mass by 17.31%, but did not reduce muscle mass. Neither preventing climbing nor reducing cage size affected anxiety assessed in the Open Field test and the Elevated Plus Maze. We did not find any negative effect of inactivity on spatial learning and memory in the novel object location test or working memory measured with the Y-maze Alternation test. The reduced physical fitness and increase in visceral fat mass show that our inactivity method models most effects of physical inactivity that are observed in experimental and observational studies in humans. Whereas established methods such as hindlimb unloading mimic many of the effects of bed rest, our novel method can be applied to study the effects of less extreme forms of physical inactivity (i.e., sedentary behavior) in various disease models including rodent models for brain diseases (i.e., stroke, Alzheimer's disease).