Lichens are symbiotic organisms composed of at least one fungal and one algal species. They are found in different environments around the world, even in the poles and deserts. Some species can withstand extreme abiotic conditions, including radiation and the vacuum of space. Their chemistry is mainly due to the fungal metabolism and the production of several secondary metabolites with biological activity, which have been isolated due to an increasing interest from the pharmaceutical community. However, beyond the experimental data, little is known about their mechanisms of action and the potential pharmaceutical use of these kinds of molecules, especially the ones isolated from lesser-known species and/or lesser-studied countries. The main objective of this review is to analyze the bibliographical data of the biological activity of secondary metabolites from lichens, identifying the possible mechanisms of action and lichen species from Chile. We carried out a bibliographic revision of different scientific articles in order to collect all necessary information on the biological activity of the metabolites of these lichen species. For this, validated databases were used. We found the most recent reports where in vitro and in vivo studies have demonstrated the biological properties of these metabolites. The biological activity, namely anticancer, antioxidant, and anti-inflammatory activity, of 26 secondary metabolites are described, as well as their reported molecular mechanisms. The most notable metabolites found in this review were usnic acid, atranorin, protolichesterinic acid, and lobaric acid. Usnic acid was the most investigated metabolite, in addition to undergoing toxicological and pharmacological studies, where a hepatotoxicity effect was reported due to uncoupling oxidative phosphorylation. Additionally, no major studies have been made to validate the pharmacological application of these metabolites, and few advancements have been made in their artificial growth in bioreactors. Despite the described biological activities, there is little support to consider these metabolites in pharmaceutical formulations or to evaluate them in clinical trials. Nevertheless, it is important to carry out further studies regarding their possible human health effects. These lichen secondary metabolites present a promising research opportunity to find new pharmaceutical molecules due to their bioactive properties.