Where is the fuel pump and fuel filter on a 1999 Honda Where is the fuel pump and fuel filter on a 1999 Honda civic ex located? The pump is in the tank. and the filter is next to the battery on top. 1999 Honda Civic fuel filter? Yes it has one. Amazon: 1999 honda civic fuel filter: Automotive 1-24 of 119 results for Automotive: "1999 honda civic fuel filter" Skip to main search results Amazon Prime. Eligible for Free Shipping. MUCO New 255LPH High Flow Intank Electric Fuel Pump with Strainer/Filter + Rubber Gasket/Hose + Stainless Steel Clamps + Universal Connector Wiring Harness MCP-203A. 3.7 out of 5 stars 40.