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I recently got my 93 Civic EX and was told you would need a jump to start it. Later found out that this was not the case. It will start fine, but after turning it off, you have to wait 10 or 15 minutes before it will start again. It will crank, but it won't actually start. I replaced the battery, which seemed to help a little. Also replaced the main relay, as I've seen a lot about that being a common problem with Hondas... At first, it seemed like the main relay didn't help. Today, it drove better, and it also started after being shut of several times with no problems... But a couple hours later it was back to the same old thing... Distributor is brand new. Could this be a fuel pump/filter problem or a timing problem? Please help, I'm absolutely stumped on what is wrong here :/ A lot of people keep telling me it's the starter, but I don't understand why or how since it's still cranking.

 
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http://www.gomog.com/starter.htm#battery

Sometimes you can get a dying starter to work by banging it with a hammer, it works still..

I honestly think you need to have the battery tested, it may not be giving you enough cranking amps

 
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Did you solve the problem? I've had a similar issue with two Civics and I never found exactly what was causing it. My best advice was that the electronic adjustments to the injectors and the ignition as the engine cools or warms is the most cause. As you mentioned, after waiting for a few minutes the car starts and runs fine. If you've found exactly what causes the problem, I'd love to hear what it is!

 
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You probably eliminated the most likely cause when you changed the relay. Isn't that fun? These seem to be designed for service by a three handed contortionist with long arms who doesn't mind standing on his head while working and doesn't need any light to see whats way up there under the drivers side panel.

So, if that didn't fix it, then the next step is to find out why it won't start. It is either no fuel or no spark and you need to know which.

Spark is pretty easy to check for. Pull one of the spark plug wires at the spark plug and put a #2 phillips screwdriver in the connector-boot that goes on the plug. Place it where the metal from the screwdriver is a 1/4 inch or less from a ground, like a valve cover nut, and have someone turn the engine a few times. If you see an arc between the screwdriver metal and the ground, you have spark and the problem is fuel.

Alternately, you can spray a short burst (no more than 1-2 seconds) of starting fluid in the air intake and crank it over. If it catches, even for a bit, then the problem is no fuel.

If the problem is no spark, there are lots of places to look. I have seen ignition switches fail such that there is no spark in the start position, but they are fine in the run position.

If its fuel, then it is likely still electrical but the culprit is probably in the injection pump circuit.

Anyway- find out whether it is no spark or no fuel, and that will give you a clue where to go next.

Since this happens after you shut it off, and waiting a few minutes makes it work again, it is likely something that is temperature sensitive, like a loose or frayed connection, bad switch, or bad relay.

The Honda relays that fail usually fail at the solder joints in an intermittent temperature sensitive way,and not in the relay itself. You can often pull the metal cover off the relay, reheat and reflow the solder, reassemble it, and often they work just fine again. I have known folks to have success with this, but I've never tried it because they are way too hard to get in and out. I'd rather just cough up for a new one then redo the job if it doesn't work.

 
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The same thing happened to my 92 EX I replaced the capacitors in my ECU(<$5) or you could just replace the whole ECU($$$) Soldering is required!