Prayer is by far one of the hardest skills to train up. Each of the “old” skills boasted at least one level 99 before someone finally reached 99 prayer. To train prayer, all you have to do is bury bones. There are several methods to obtain bones after using them. The fastest option without running is to use a worn Ring of dueling, Amulet of glory, Ring of kinship, or a TokKul-Zo to teleport to a bank. For free players, the only fast way of prayer is to buy loads of big bones from the Grand Exchange. Also, for free players, you can go to the Chaos Temple. There are many bones that respawn there. What you can do is go to world 1 and collect all 11. Then bury them.
Kill giants is another good way to train prayer skill. At combat level below 50, you should train with level 28 Hill Giant in Edgeville Dungeon. This will be a bit sucked since there are a lot of people killing Hill Giant all the times. Above level 50, you should train with level 42 Moss Giant in VarrockSewer. Around 2-5 PM, almost all worlds are quiet enough to train with them alone. Don’t ever try to train with it at wilderness unless you have a death with.
Finally, perhaps you can consider buying a runescapeaccount which has high prayer skill (for example on farmer100). In this way you don’t need to train prayer skill. It saves you a lot of time.