We expound the notion of “distinct experience” (experientia distincta) as introduced in the writings of the early modern polymath Joachim Jungius (1587–1657) and operative in his scientific practice. After contextualizing “distinct experience” historically (e.g., vis-à-vis Francis Bacon’s [1561–1626] concept of “experience”) and embedding the notion conceptually into the broader category of “division” (divisio), we reconstruct the “Problem of Distinct Experience”: Jungius’ epistemology of science involves a circularity or an infinite regress because scientific methods (inductions and demonstrations) presuppose divisions, which are, in turn, built on distinct experiences, themselves presupposing divisions. However, we argue through a careful historical case study on his investigations of fossilia that his research practice shows why the problem posed only a limited threat for him and his contemporaries. We finish with a brief philosophical appraisal, contrasting his views with those of Jacopo Zabarella (1533–1589).