El Salvador Peace, Security, Justice, and Democracy Act of 1990

El Salvador Peace, Security, Justice, and Democracy Act of 1990 - Limits the amount of military assistance for El Salvador for FY 1991. Prohibits the provision of such assistance if the El Salvadoran Government: (1) declines to participate in negotiations with the Farabundo Marti National Liberation Front (FMLN) to terminate hostilities; (2) fails to support an active role for the United Nations Secretary General in such negotiations; (3) fails to conduct an investigation into, and prosecution of, those responsible for the murders at the University of Central America; and (4) has not taken steps to separate the law enforcement forces from the armed forces and to protect the constitutionally guaranteed activities of all groups in El Salvador.

Limits the amount of El Salvador military assistance to be obligated between specified dates in FY 1991. Withholds certain percentages of such funds from obligation and covers them in a separate escrow account. Authorizes the President to release such funds (for purposes of reconciliation, cease-fire monitoring, and repatriation and reemployment of former members of the El Salvadoran armed forces and the FMLN) when negotiations to terminate the armed conflict and to reintegrate the FMLN forces into Salvadoran society have been completed. Makes FY 1991 military assistance available to El Salvador unconditionally if the FMLN: (1) declines to participate in negotiations or to support the Secretary General's role in such negotiations; (2) conducts a sustained military offensive which increases risks to El Salvadoran noncombatants; (3) fails to cooperate in investigating and prosecuting FMLN members responsible for human rights abuses; and (4) is continuing to receive significant quantities of lethal military equipment from outside El Salvador.

Prohibits U.S. military assistance from being obligated by the armed forces without the approval of the elected president of El Salvador.

Directs the Secretary of State, through an agreement with the National Endowment for Democracy, to carry out a program to strengthen democratic political and legal institutions in El Salvador. Authorizes appropriations.