We performed a quantum-mechanical study of the effect of antiphase boundaries (APBs) on structural, magnetic and vibrational properties of FeAl compound. The studied APBs have the {001} crystallographic orientation of their sharp interfaces and they are characterized by a 1/2〈111〉 shift of atomic planes. There are two types of APB interfaces formed by either two adjacent planes of Fe atoms or by two adjacent planes containing both Fe and Al atoms. The averaged APB interface energy is found to be 80 mJ/m and we estimate the APB interface energy of each of the two types of interfaces to be within the range of 40–120 mJ/m. The studied APBs affect local magnetic moments of Fe atoms near the defects, increasing magnetic moments of Fe atoms by as much as 11.8% and reducing those of Fe atoms by up to 4%. When comparing phonons in the FeAl with and without APBs within the harmonic approximation, we find a very strong influence of APBs. In particular, we have found a significant reduction of gap in frequencies that separates phonon modes below 7.9 THz and above 9.2 THz in the defect-free FeAl. All the APBs-induced changes result in a higher free energy, lower entropy and partly also a lower harmonic phonon energy in FeAl with APBs when compared with those in the defect-free bulk FeAl.