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<i>Cichorium endivia</i> L. (Asteraceae) is a wide edible plant that grows in the Mediterranean region. In this study, a phytochemical investigation of <i>C. endivia</i> L. ethanolic extract led to the isolation of stigmasterol (<b>1</b>), ursolic acid (<b>2</b>), <i>β</i>-amyrin (<b>3</b>), azelaic acid (<b>4</b>), vanillic acid (<b>5</b>), (6S, 7E)-6-hydroxy-4,7-megastigmadien-3,9-dione (S(+)-dehydrovomifoliol) (<b>6</b>), 4-hydroxy phenyl acetic acid (<b>7</b>), vomifoliol (<b>8</b>), ferulic acid (<b>9</b>), protocatechuic acid (<b>10</b>), kaempferol (<b>11</b>), <i>p</i>. coumaric acid (<b>12</b>), and luteolin (<b>13</b>). In addition, the total phenolic content as well as the in vitro antioxidant activity of <i>C. endivia</i> L. extract were estimated. Moreover, we inspected the potential gonado-protective effect of <i>C. endivia</i> crude extract, its phenolic fraction, and the isolated coumaric, vanillic, and ferulic acids against methotrexate (MTX)-induced testicular injury in mice. There were seven groups: normal control, MTX control, MTX + <i>C. endivia</i> crude extract, MTX + <i>C. endivia</i> phenolic fraction, MTX + isolated coumaric acid, MTX + isolated vanillic acid, and MTX + isolated ferulic acid. MTX was given by i.p. injection of a 20 mg/kg single dose. The crude extract and phenolic fraction were given with a dose of 100 mg/kg/day, whereas the compounds were given at a dose of 10 mg/kg/day. A histopathological examination was done. The testosterone level was detected in serum together with the testicular content of malondialdehyde (MDA), catalase (CAT), superoxide dismutase (SOD), interleukin 1β (IL-1β), IL-6, tumor necrosis factor alpha (TNF-α), nuclear factor kappa B (NF-κB), B-cell lymphoma 2 (Bcl-2), Bcl-2 associated x protein (Bax), p53, and miR-29a. <i>C. endivia</i> crude extract, the phenolic fraction, and the isolated compounds showed significant elevation in their levels of testosterone, CAT, SOD, Bcl-2 with a significant decrease in their levels of MDA, TNF-α, IL-1β, IL-6, NF-κB, Bax, P53, and miR-29a compared to those of the MTX control group. In conclusion, <i>C. endivia</i> mitigated MTX-induced germ cell toxicity via anti-inflammatory, antioxidant, and antiapoptotic effects.