Most of the novels can be read independently of the others. However, the first three listed below are best read in sequence since they deal with the saga of a single family, in order as follows:

1) Strangers and Sojourners (1997)
2) Eclipse of the Sun (1998)
3) Plague Journal (1999)

4) Father Elijah: an apocalypse (1996)
5) Sophia House (2005)
6) A Cry of Stone (2003)

Sophia House is a "prequel" to Father Elijah, but the order in which these two are read does not matter. The latter three (4,5,6) can be read in any sequence.

Three other novels are not officially part of the Children of the Last Days series:

7) The Island of the World (2007)
8) Theophilos, (2010)
9) The Father's Tale (2011)