The success of pulpotomy of young permanent teeth depends on the proper selection of dressing materials. This study aimed to evaluate the histological and histomorphometric response of dentin–pulp complex to the enamel matrix derivative (Emdogain® gel) compared to that of calcium hydroxide when used as a pulp dressing in immature young permanent dogs’ teeth. Dentin-like tissues bridging the full width of the coronal pulp at the interface between the injured and healthy pulp tissues were seen after 1 month in both groups. With time, the dentin bridge increased in thickness for calcium hydroxide but disintegrated and fully disappeared for Emdogain-treated group. Progressive inflammation and total pulp degeneration were only evident with Emdogain-treated group. The root apices of Emdogain-treated teeth became matured and closed by cementum that attached to new alveolar bone by a well-oriented periodontal ligament. In young permanent dentition, Emdogain could be a good candidate for periodontium but not dentino–pulpal complex regeneration.