He was originally supposed to become a businessman, but in accordance with his aptitude Baehrens attended the Friedrich-Wilhelm-Gymnasium in Cologne.
Most influential on Baehrens was Lucian Müller, as well as Otto Jahn and Hermann Usener, who gave him metrical and paleographical exercises, which brought him in 1868 to the Philological Seminar.
Finally, he undertook his first educational trip, where he saw antique manuscripts in Munich, Milan, Bologna, Pisa, Venedig, Florence, Lucca, Siena, Rome, and Naples.
After his return in the autumn of 1873 Baehrens qualified as a professor at the Friedrich-Schiller-Universität Jena with the article "De Sulpiciae quae vocatur satira, commentatio philologica".
During his research, Emil Baehrens brought forth many important editions of different Latin authors, including Catullus ("Catulli Veronensis liber", 1876, with a large commentary published as second volume in 1885), "Panegyrici Latini", Gaius Valerius Flaccus ("C. Valeri Flacci Setini Balbi Argonauticon libri octo"), Publius Papinius Statius ("Silvae"), Tibullus ("Tibullinische Blätter"), Sextus Propertius, Horace ("Lectiones Hortianae"), Tacitus ("Dialogus de oratoribus"), and Minucius Felix ("Octavius").