Background: The epidemiology of atopic eczema in adolescents in Kosovo is virtually unknown, and the risk factors for the condition in very low-prevalence areas (as it was the case) are not well studied. The objective of the present study was to better know those factors and whether the presence of comorbid wheezing symptoms modifies the factors. Methods: The cross-sectional survey, Global Asthma Network-validated questionnaire, which includes questions on eczema symptoms and environmental factors (such as smoking, pet ownership, paracetamol usage, truck traffic, siblings, time spent using screens or watching television, and physical exercise), was administered to adolescents in the following main cities of Kosovo: Ferizaj, Gjakova, Gjilan, Peja, Prishtina, and Prizren. Additionally, height and weight were measured at school. Results: Prevalence of eczema symptoms ranged from 2.2% in Ferizaj to 5.5% in Gjakova. Severe symptoms were <1% in all cities. Eczema ever ranged from 3.0% in Ferizaj to 6.4% in Prizren. Factors significantly associated with the prevalence of current eczema symptoms in the meta-analysis were males (pooled adjusted odds ratio [aOR] 0.50, 95% Confidence Interval [95% CI] 0.37–0.66); physical exercise (pooled aOR 2.79, 95% CI 1.89–4.10); and paracetamol intake (pooled 1.86, 95% CI 1.32–2.64). The corresponding figures for eczema ever were as follows: pooled aOR: 0.68, 95% CI 0.44–1.06; pooled aOR 2.07, 95% CI 1.48–2.90; and pooled aOR 1.19, 95% CI 0.88–1.60. The associations tended to be higher in the subpopulation with eczema and wheezing comorbidity. Conclusions: The prevalence of atopic eczema is very low in Kosovo and is associated with females, physical exercise, and paracetamol intake. These associations are higher when eczema and wheezing are comorbid conditions.