Objectives: We sought to evaluate the effectiveness of six weeks pulmonary rehabilitation (PR) in patients with asthma-chronic obstructive pulmonary disease (COPD) overlap syndrome (ACOS). Methods: We enrolled 28 patients with ACOS. Fourteen patients were randomly allocated to the PR group, which comprised of supervised endurance training, supervised resistance training, breathing exercises, self management, and education. The other 14 patients were allocated to the control group, who were asked to continue their usual routine strategies for six weeks. All patients were assessed at baseline and after six weeks using the six minute walk test (6MWT), St George Respiratory Questionnaire (SGRQ), pulmonary function test (PFT), and Bode index (BI). Results: We saw a significant improvement in 6MWT (p = 0.001), SGRQ (p = 0.007), and BI (p < 0.001) in the PR group after six weeks compared to the control group. There was no significant difference between the groups for PFT (p = 0.182) after six weeks. Conclusions: Use of a short-term PR program in ACOS patients results in favorable changes in functional capacity, health-related quality of life, and BI. However, short-term PR was not sufficient to register changes in pulmonary function in these patients.