1999 Honda Accord New battery Alternator checked at Auto Zone and Advance auto put alternator back on car still batery still goes dead in about 30 miles

Yes you could have an ECU problem but there are a number of tests that need to be done. I have found in a couple of the accords to be an open wire. Below is a picture of the connector at the alternator. Unplug it and turn the key to the on position (make sure your battery is fully charged) check the number 1 position of the plug. There should be battery voltage there. If there isn't you need to locate the open black & yellow wire. That wire should go directly to the fuse box inside the vehicle. This has happened a couple of times in my shop. You could have other problems but would try this first. If all is well with this tests feel free to email me at [email protected] with all your information and I will be happy to give you some other tests to perform in order to narrow down the problem. No there wouldn't be a charge for my help, don't mind helping when I can. As long as you can kinda follow and locate wires/connectors and have a digital volt/ohm meter (and know how to use it) I think narrowing down the problem will be fairly easy. On this picture I am going by that you have the most common engine (4 cylinder 2.3) If you have the DV or LX model with the V6 3.0 liter engine there may be a difference so this test might not be correct. Was just going with the common engine. Hope this helps......