I have a FAQ category and there are posts in that category I want to add pagination to that category only, not the other category in my wordpress.
In short giving pagination to selected category for the posts in that category
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category-faq.php in your theme folder ( assuming category is your taxonomy and faq is the term slug ), and put your category code in there, and add pagination code to that file. This is a category specific template.
For a view of what templates you can add and the types of instances they occur in and their fallbacks, refer to this image:
I would highly suggest usting custom templates for this; a good tutorial can be found here: http://www.vooshthemes.com/blog/wordpress-tip/create-a-professional-portfolio-using-wordpress-3-0-custom-post-types/
If you don't go the custom templates route you're going to need to create a template for that specific category - as mentioned above name it category-name.php... "name" should be replaced with the name of your category.
You can do the pagination with this plugin: http://wordpress.org/extend/plugins/wp-paginate/
Alternatively, you can used WP's built-in pagination function: http://codex.wordpress.org/Function_Reference/paginate_links