Do Noragami anime and manga share the same story line? I have finished watching Noragami anime. Then I saw the Noragami manga. The anime has only 12 episodes but manga is ongoing. So if I want to read the manga from which chapter should I start? I mean after anime episode 12.
Do Noragami anime and manga follow the same storyline?

Yes, mostly.


Noragami Ep 1-9 and beginning of 10 are canon.
Noragami Aragoto Ep 1-6 are canon.


Noragami covered around the first 3 volumes of the manga, which covers the introduction of the 3 main characters. 

Where should I start to read after episode 12 of Noragami?

Considering Noragami covers roughly 3 volumes, you could start at chapter 12, the first chapter of volume 4.

The full canon view/reading order as told by blessedyiki's tumblr 


Noragami (Ep 1-9 and beginning of 10)
Noragami Aragoto (Ep 1-6 (you might want to read Chapter 23 for the full Kazuma/Ma clan backstory) 
Noragami Aragoto Episode 7 right until the opening 
Noragami OVA 2 
Noragami OVA 1 
Noragami Aragoto Episodes 7-13 
Chapter 40 
Noragami Aragoto OVA 2.