Is there any way to transfer funds thru internet from one bank to another bank which doesn't have MICR code ?

Answer 1

If you're talking about different banks with the same account holder........... that's not a problem.

Two banks that I deal with;
GMACBank.com & EverBank.com both have systems to allow this (as I'm sure other banks do).

If you're looking to send money to someone other than yourself (or co-owner)...... most banks allow you to use "bill pay". A check is issued and mailed (with MICR) at no charge (for check or postage).

The most popular method is "Wire" the funds. This is a direct bank to bank / account to account method. Usually there's a charge of $25 (+/-).

Hope that answers your question.