Railway Safety and Funding Equity Act of 1999

Railway Safety and Funding Equity Act of 1999 - Amends Federal transportation law to authorize to be appropriated out of the Highway Trust Fund (HTF) (other than the Mass Transit Account) for each of FY 2000 through 2003 to carry out projects for the elimination of hazards of railway-highway crossings and projects for the elimination of railway-railway crossings an amount determined by the Secretary of the Treasury to be equivalent to the total of amounts received in the Treasury in the previous fiscal year that are attributable to taxes imposed on fuel used in a train.

Sets forth provisions regarding apportionment of funds. Directs that at least five percent of sums available to a State in a fiscal year be expended on education and awareness campaigns, and that at least ten percent be expended on projects for the elimination of railway-railway crossing hazards. Sets the Federal cost share at 80 percent.

Amends the Transportation Equity Act for the 21st Century to exclude such funding from the obligation ceiling for Federal-aid highway and highway construction programs.

(Sec. 3) Amends the Internal Revenue Code to: (1) transfer the excise taxes on fuel used in trains to the HTF beginning on October 1, 1999; and (2) terminate such excise taxes on October 1, 2004.