I have a 1999 Honda Civic manual transmission. 1.6 litter.
I have a starting problem. I have replaced the fuel pump and fuel filter. Sometimes the car starts up immediately and sometimes it takes 2-3 try’s (4-5 secs cranking). It is worse with fuel is low.
You may have installed a defective fuel pump out of the box.
The next time the engine won’t start, turn the ignition switch off. Then turn the ignition switch to the run position for two seconds and then turn it off.
Repeat this a half dozen times and then try starting the engine. If the engine starts right up, that new fuel pump is defective.
The '99 Civics are under a Recall for faulty ignition switches. The symptoms can vary from intermittent stalling to no starts, etc.
Call the local Honda dealer with your VIN and verify that you’re covered. This repair can be done free of charge for you.
There’s other possibilities such as the main relay, etc but seeing as how the switch is free take advantage of that and see if it fixes the problem.
I would change the main fuel relay in any event. They have been troublesome for Honda’s for many years. Your Civic falls right in the middle of the problem years. Inexpensive and easy to replace.
When you turn the key from Off to Run, the fuel pump should run for a couple seconds. If you listen in a quiet place, you may hear it run. If it runs, the ignition switch and the relay have worked as they should. Repeating the Off-Run cycle a couple times builds up fuel pressure, so there’s enough fuel and pressure to enable the engine to start.