In the past, neighbors were concerned about Uganda's relationship with Libya, which had supplied military equipment and bartered fuel to Uganda. In addition to its friendly ties to Western nations, Uganda has maintained ties with North Korea. Uganda's has strained relations with Sudan because of past Sudanese support for the LRA. The LRA seeks to overthrow the Uganda Government and has inflicted brutal violence on the population in northern Uganda, including rape, kidnapping, torture, and murder. In 2002 Uganda and Sudan reestablished diplomatic ties and signed a protocol permitting the UPDF to enter southern Sudan and engage the LRA. The protocol must be renewed periodically.

Another rebel group operating in western Uganda and eastern Democratic Republic of the Congo, near the Rwenzori Mountains, the Allied Democratic Forces (ADF), emerged as a localized threat in 1996 and inflicted substantial suffering on the population in the area. It has largely been defeated by the UPDF and the affected areas of western Uganda have been secured. Remnants of the ADF remain in eastern Congo.