You can run commands either in game in the chat or via RCON.
In Game Chat Box (Use / to begin each command):

| addalltowhitelist | Adds all currently connected users to the whitelist | /addalltowhitelist |
| additem | Gives an item to a specified player | /additem user module.item |
| adduser | Adds a user to the whitelist | /adduser username password |
| addusertowhitelist | Adds a user connected with a password to the whitelist | /addusertowhitelist user |
| addvehicle | Spawns a vehicle | /addvehicle user |
| addxp | Gives XP to the specified player | /addxp user perk=XP |
| alarm | Sounds a building alarm at the position of the admin. Must be indoors. | /alarm |
| banid | Bans a player based on their Steam ID | /banid SteamID |
| banuser | Bans a player based on their username | /banuser user |
| changeoption | Changes a server option | /changeoptions open=newOption |
| chopper | Places a helicopter event on a random player. | /chopper |
| createhorde | Spawns a horde near a player | /createhorde number |
| godmode | Makes the specified user invincible | /godmode user |
| gunshot | Makes a gunshot noise near the player | /gunshot |
| help | Displays the help menu | /help |
| invisible | Makes the specified player invisible to zombies | /invisible user |
| kickuser | Kicks the specified user from the server | /kick user |
| noclip | Allows the specified player to pass through solid objects and walls | /noclip user |
| players | Lists all players currently on the server | /players |
| quit | Saves and stops the server | /quit |
| releasesafehouse | Releases a safehouse that you own | /releasesafehouse |
| reloadoptions | Reloads the server options | /reloadoptions |
| removeuserfromwhitelist | Removes the specified user while connected from the whitelist | /removeuserfromwhitelist |
| replay | Records and plays a replay for a moving player | /replay user [-record, -play -stop] filename |
| save | Saves the world | /save |
| sendpulse | Toggles sending server performance info to the client | /sendpulse |
| servermsg | Sends a message to all players on the server | /servermsg message |
| setaccesslevel | Set the permission level of a player | /setaccesslevel user [admin, moderator, overseer, gm, observer] |
| showoptions | Shows all current options and values | /showoptions |
| startrain | Starts rain on the server | /startrain |
| stoprain | Stops rain on the server | /stoprain |
| teleport | Teleport user to user or to a user | /teleport toUser , user toUser |
| teleportto | Teleport to specified coordinates | /teleportto x,y,z |
| unbanid | Unbans a user based on their Steam ID | /unbanid SteamID |
| unbanuser | Unbans user based on their username | /unbanuser username |
| voiceban | Bans user from using voice chat | /voiceban user [-true, -false] |