Thymus longicaulis C. Presl. (Lamiaceae) is a small aromatic perennial herb typical of the Illyric-Mediterranean flora, traditionally used as remedy for cold, flu, cough, nephritis and abdominal pain. In order to carry out a thorough chemical and biological screening of the plant and to explore phenophases influence on its polyphenol content, samples of the plant were collected at different phases during its life cycle (July/October 2012 and January/April 2013). Each sample, previously extracted using a hydroalcoholic solution, was phytochemically analyzed for its metabolic constitution applying LC-DAD-ESI-MS/MS techniques. Although identified metabolites were differently concentrated at the various collection times, T. longicaulis leaf extracts were mainly constituted by low molecular weight phenols, and flavonoids. Rosmarinic acid was found as the main metabolite in Oct12 sample. Chemopreventive efficacy of the investigated extracts, by means of their anti-inflammatory, cytotoxic and antioxidant activities, was assessed. To this purpose, each extract underwent an extensive screening towards five human cell lines: CCRF-CEM (leukemia); U251 (glioblastoma); MDA-MB-231 (breast cancer); HCT-116 (colon cancer) and MRC-5 (lung fibroblasts) through XTT [2,3bis(2-metoxy-4-nitro-5-sulfophenyl)-5-[(phenylamino)carbonyl]-2H tetrazolium hydroxide] test. The ability of the extracts to counteract cyclooxygenase-2 (COX-2) expression was also evaluated by COX-2 expression assay in human THP-1 monocyte-derived macrophages. COX-2 inhibition could represent a valuable anticancer strategy as it is associated with carcinogenesis and over-expressed in a variety of human malignancies. Oct12 extract, which was particularly rich in rosmarinic acid and methylapigenin, exhibited a strong antioxidant and anti-inflammatory effectiveness.