A partial order is universal if it contains every countable partial order as a suborder. In 2017, Fiala, Hubička, Long and Nešetřil showed that every interval in the homomorphism order of graphs is universal, with the only exception being the trivial gap $[K_1,K_2]$. We consider the homomorphism order restricted to the class of oriented paths and trees. We show that every interval between two oriented paths or oriented trees of height at least 4 is universal. The exceptional intervals coincide for oriented paths and trees and are contained in the class of oriented paths of height at most 3, which forms a chain.