The BTR-4E Bucephalus can be fitted with different types of weapon stations, but the standard version is fitted with a remotely operated weapon station called BM-3 Shturm which is armed with one ZTM-1 30mm automatic cannon. The second armament of the turret includes one KT or PKT 7.62mm machine gun, and one AG-17 30mm automatic grenade launcher mounted to the left side of the main armament. Two launchers for the Anti-Tank Guided Missile (ATGM) Barrier are fitted to the right side of the turret. The Barrier missile uses a semi-automatic laser beam guidance system. The warhead of the Barrier missile can penetrate ERA (Explosive Reactive Armour) up to 800mm. It can hit a target from a distance of 100 to 5,000m. The turret is operated by the gunner from inside of the hull, on a seat located on the right side of the troop's compartment. The commander of the vehicle can take control of all the weapons of the turret, thanks to its individual screen and a joystick located at the front of its seat. Mounted on either side of the main armament is a bank of three electrically operated smoke grenade launchers. The BTR-4E can be fitted with the weapon stations BM-7 Parus, BM Grom, and BAU 23-2.

The design of the BTR-4E Bucephalus is divided into three compartments with driver and commander seats at the front, engine and transmission in the middle, and troops compartment at the rear. The vehicle has a crew of three and seven infantrymen that can be carried at the rear of the vehicle. The infantrymen enter and leave the BTR-4E via a double door at the rear of the hull, which opens outwards. The right door is fitted with a single firing port. Each soldier has an individual seat facing inwards, with four seats mounted on each side of the hull. Each rear part of the side hull is equipped with three firing ports and day vision devices mounted on the roof. The driver sits at the front of the vehicle on the left with the commander to his right. Both crew members have a side door that opens to the front, with a bulletproof window in its upper part hinged at the top. The commander and gunner have a single-piece hatch on the roof of the vehicle that opens to the front. Both the commander and driver have also a bulletproof window to their front which is covered in combat by an armored plate cover hinged at the top. The BTR-4E hull is protected against the firing of small arms 7.62mm AP (Armour Piercing) caliber and artillery shell splinters, Level 2 STANAG 4569. The BTR-4E is also equipped with an anti-mine "skirt" which improves protection against mine blasts and IEDs (Improvised Explosive Devices). To increase the protection of the vehicle, the turret and the sides can be fitted with slat armor to provide a higher level of protection against attack by rocket-propelled grenades and other weapons fitted with a HEAT warhead. There is also an add-on armor kit available that can provide all-around protection against weapons of 30mm caliber.