P46 contains the Epistles of Paul, in the following order:
| Pages: | Contents: |
| 1-41 | Romans |
| 41-64 | Hebrews |
| 64-117 | 1 Corinthians |
| 118-145 | 2 Corinthians |
| 146-158 | Ephesians |
| 158-168 | Galatians |
| 168-176 | Philippians |
| 176-184 | Colossians |
| 184-191 | 1 Thessalonians |
| 191-195 (?) | 2 Thessalonians (?) |
| 195-205 (?) | Uncertain |
The order of the epistles is different than in the modern text, but reflects the Egyptian views of the time, placing an emphasis on the importance of Hebrews. The authenticity of Hebrews is debated to this day, and at the time when P46 was written it was generally rejected in the West, while in Egypt and the East it was considered a genuine Epistle of Paul.
As mentioned, 86 of 104 original leaves survive today. The missing leaves account for pages 1-13, 16-19, 186-189, and 192-205. The contents of the first three of these gaps can easily be determined because they fit into a portion of the codex whose contents are known. However, the final fourteen pages of the codex have given scholars some difficulty. It seems fairly likely that, along with the damaged portion of page 191, four of these (pages 192-195) would have contained 2 Thessalonians. The remaining ten pages are too small a space to hold the Pastoral Epistles; it is always possible that these pages were simply blank, or perhaps that extra pages were added to hold the Pastoral Epistles. Since the end of the codex is lost, the true answer will never be known.