The paired t-test and the Wilcoxon signed-rank test are often conducted to compare two continuous outcomes from paired observations. An assumption underlying these tests is that the responses from pair to pair are mutually independent. However, the assumption is violated in certain applications such as site-specific data in periodontal research. An adjustment to the paired t-test to account for the clustering effect has been well developed. But the adjustment relies on either large sample theory or the assumption that the observations being analyzed follow a normal distribution. In this paper, we propose a permutation test for matched pair clustered data which are valid in small samples. We developed and reviewed software to carry out the proposed test. The proposed test is applied to real-life data.