Primary weapon for the Type 039 is the 533 mm Yu-4 torpedo, a locally produced passive homing 40-knot (74 km/h) torpedo based on the SAET-50 and roughly comparable to the SAET-60. Surface targets may be attacked at up to 15 km. Yu-6 wire-guided torpedoes may also be used for targeting submarines.

It is also likely that the Type 039 is capable of carrying the YJ-8 anti-ship missile, a cruise missile which can be launched from the same tube as the boat’s torpedoes, and can target surface vessels at up to 80 km.

The missile is subsonic and carries a 165 kg warhead. For mining operations, in place of torpedoes, the submarine can carry 24 to 36 naval mines, deliverable through the torpedo tubes.