One can Register .edu Domain Name only after meeting some certain Eligibility criteria. Here are Eligibility criteria for .edu domains.
let's come to your questions.
1.) How to register .edu domain in Pakistan?
Ans: You cannot register .edu domain in Pakistan. Any individual cannot register any .edu domain. There must be an organization/institutions related to Education in US. Check more about eligibility criteria for .edu domains.
2.) Where to register .edu domains in Pakistan?
Ans: As stated above, you cannot register .edu domains in Pakistan. You can Register .edu.pk in Pakistan.
Check out: How to Register .edu Domain in India?