In recent decades, the application of experimental modal identification tests in civil engineering structures is gaining interest for various purposes such as model calibration, quality control while the construction process, damage detection, and structural health monitoring of new buildings and bridges. The use of these tests in archaeological earthen sites is a novel area of application. The paper presents the results of operational modal analysis tests carried out on an archaeological site in Peru as part of an extensive research for assessing its structural vulnerability. The case study is related to the tests on one of the remaining stone masonry walls of Chokepukio archaeological site, which dates back to the twelfth century. The paper shows a brief summary of the historical condition of the site, the details of the tests carried out, the experimental data processing results, as well as the Finite Element model updating process using manual and automatic routines.