Smoking Cost Recovery and Education Tax Act of 1988 - Amends the Internal Revenue Code to increase the excise tax on cigarettes from: (1) $8 to $20.50 per thousand for small cigarettes; and (2) $16.80 to $43.05 per thousand for large cigarettes.

Establishes in the Treasury the Smoking Cost Recovery and Education Trust Fund, to be available to finance educational programs (including paid advertising) concerning the hazards of cigarette smoking, with emphasis on discouraging smoking by youth. Appropriates to the Fund ten percent of the tobacco tax revenue generated by this Act's rate increase.

Directs the Secretary of the Treasury to conduct an ongoing study and to report biennially to specified congressional committees on: (1) the effects of smoking on health care costs; and (2) the incidence of cigarette smoking by youth, including the relationship between cigarette tax rates and youth smoking.