Quantum control of motion is central for modern atomic clocks1 and interferometers2. It enables protocols to process and distribute quantum information3,4, and allows the probing of entanglement in correlated states of matter5. However, the motional coherence of individual particles can be fragile to maintain, as external degrees of freedom couple strongly to the environment. Systems in nature with robust motional coherence instead often involve pairs of particles, from the electrons in helium, to atom pairs6, molecules7 and Cooper pairs. Here we demonstrate long-lived motional coherence and entanglement of pairs of fermionic atoms in an optical lattice array. The common and relative motion of each pair realize a robust qubit, protected by exchange symmetry. The energy difference between the two motional states is set by the atomic recoil energy, is dependent on only the mass and the lattice wavelength, and is insensitive to the noise of the confining potential. We observe quantum coherence beyond ten seconds. Modulation of the interactions between the atoms provides universal control of the motional qubit. The methods presented here will enable coherently programmable quantum simulators of many-fermion systems8, precision metrology based on atom pairs and molecules9,10 and, by implementing further advances11-13, digital quantum computation using fermion pairs14.