The story appears to be set in contemporary March 2009 (as evidenced by the various calendars on the walls and this page-a-week diary in Claire's room)
There are, however some very dramatic changes to our own timeline, primarily that the world (which bears only a passing similarity to ours in terms of geography) has gone through some sort of major confrontation, generally described simply as "The War". This confrontation between good and evil took place some 16 years hence, with Witches on one side and Nuns on the other. The War itself ended dramatically when the enemy witches simply vanished on the same day that Claire was given over to the care of the nuns.
The world outside the nunnery is presented as being semi-medieval, albeit with numerous anachronisms including a giant steampunk robot and the extensive use of plastics and manufactured goods such as pens.
The landscape is described by the sisters as "ravaged" and covered in "ruins". On several occasions the characters remark that their maps are now useless, suggesting an enormous social upheaval and/or an apocalyptic event, possibly connected with the War but also possibly much earlier given the state of the ruins. The landscape also seems decidedly under-populated (reference to small villages) which again strongly suggests a considerable number of deaths have occurred.