New cranial and postcranial remains of the Early–Middle Jurassic turtle, Condorchelys antiqua, are described here in detail, providing new insights into the early evolution of turtles. Unconstrained and constrained cladistic analyses in addition to newly developed total-evidence Bayesian analysis were performed to explore large-scale turtle relationships and evolutionary trends. All the analyses show a similar resolution at the base of the tree, recovering several species of small-sized, fresh water turtles of the Early–Middle Jurassic at the base of the tree following the most basal, large-sized, terrestrial turtles from the Late Triassic. The calibration of the cladistic analyses and the tip-dating analysis provided similar results in the main nodes Testudines, Pan-Cryptodira, Cryptodira, Pan-Pleurodira, and Pleurodira, corroborating that the Jurassic is a key period for turtle evolution. The significant reduction in size in Early–Middle Jurassic stem turtles and the combination of certain characters (e.g., presence of fontanelles, loss of bones, loss of scutes) shown by those taxa suggests heterochronic changes, paedomorphosis in particular, at the base of the turtle tree. These morphological novelties could have trigged, or facilitated, the occupation of the aquatic niche as seen in Jurassic stem turtles.