brown #
= weekly rock chart peak
blue #
= pop chart peak
| 1 | Red Sam | Apr 2005 |  |
| 2 | I'm So Sick | 22 | Feb 2006 | |
| 3 | Fully Alive | 28 | Jul 2006 | |
| 4 | Perfect | Jun 2007 | |
| 5 | Do You Hear What I Hear? | Dec 2007 | |
| 6 | Breathe Today | Feb 2008 | |
| 7 | All Around Me | 3 | 13 | May 2008 | |
| 8 | Sorrow | 2008 | |
| 9 | There For You | Feb 2009 | |
| 10 | Beautiful Bride | Oct 2009 | |
| 11 | Again | 4 | Jan 2010 | |
| 12 | Chasm | Jun 2010 | |
| 13 | Missing | Jun 2010 | |
| 14 | New Horizons | Sep 2012 | |
| 15 | Call You Out | Nov 2012 | |
| 16 | Fire Fire | Jan 2013 | |
| 17 | Something Better | Jul 2013 | |
| Flyleaf Featuring Sonny Sandoval |
| 18 | Set Me On Fire | 2014 | |
| 19 | Thread | 2015 | |