The BNP ruled by decree until January 1986 when a military coup forced them out of office. The Military Council that came into power granted executive powers to King Moshoeshoe II, who was until then a ceremonial monarch. In 1990, however, the King was forced into exile after a falling out with the army. His son was installed as King Letsie III.

The chairman of the military junta, Major General Metsing Lekhanya, was ousted in 1991 and then replaced by Major General Phisoane Ramaema, who handed over power to a democratically elected government of the BCP in 1993. Moshoeshoe II returned from exile in 1992 as an ordinary citizen. After the return to democratic government, King Letsie III tried unsuccessfully to persuade the BCP government to reinstate his father (Moshoeshoe II) as head of state. In August 1994, Letsie III staged a coup which was backed by the military and deposed the BCP government. The new government did not receive full international recognition. Member states of the Southern African Development Community (SADC) engaged in negotiations aimed at the reinstatement of the BCP government. One of the conditions put forward by the King for the return of the BCP government was that his father should be re-installed as head of state. After protracted negotiations, the BCP government was reinstated and the King abdicated in favor of his father in 1995, but Moshoeshoe II died in a car accident in 1996 and was again succeeded by his son, Letsie III. The ruling BCP split over leadership disputes in 1997.

Prime Minister Ntsu Mokhehle formed a new party, the Lesotho Congress for Democracy (LCD), and was followed by a majority of Members of Parliament, which enabled him to form a new government. The LCD won the general elections in 1998 under the leadership of Pakalitha Mosisili, who had succeeded Mokhehle as party leader. Despite the elections being pronounced free and fair by local and international observers and a subsequent special commission appointed by SADC, the opposition political parties rejected the results.

Opposition protests in the country intensified, culminating in a violent demonstration outside the royal palace in August 1998. When junior members of the armed services mutinied in September, the government requested a SADC task force to intervene to prevent a coup and restore stability. A military group of South African and Botswana troops entered the country in September, put down the mutiny, and withdrew in May 1999. Looting, casualties, and widespread destruction of property followed.

An Interim Political Authority (IPA), charged with reviewing the electoral structure in the country, was created in December 1998. The IPA devised a proportional electoral system to ensure that there be opposition in the National Assembly. The new system retained the existing 80 elected Assembly seats, but added 40 seats to be filled on a proportional basis. Elections were held under this new system in May 2002, and the LCD won again. For the first time, due to the inclusion of proportional seats, opposition political parties won significant numbers of seats. Nine opposition parties now hold all 40 of the proportional seats, with the BNP having the largest share (21). The LCD has 79 of the 80 constituency-based seats. Although its elected members participate in the National Assembly, the BNP has launched several legal challenges to the elections, including a recount; none has been successful.