First and foremost is that you remember you are working with heated art materials and tools where temperature can range, when properly used, in the hundreds of degrees; and unsafe temperatures when improperly used. As with all mediums taking precautions can help you prevent injury.
The temperature for working with encaustic should remain constant at or below 225°F (many trusted resources recommend a temperature of 220°F). Temperatures above 250°F cause beeswax to breakdown; encaustic can off-gas dangerous vapors such as formaldehyde, and acrolein. For boiling points of beeswax and other waxes used, see Temperatures (Melting and Flash Point).
Make certain that the temperature of your palette can be regulated and kept at a constant temperature. The rheostat that controls this on most hotplates and burners can be or become faulty; it is imperative that you stay aware of this. If you believe that the temperature fluctuates beyond your control, immediately replace the hotplate/burner with one that does not.
Encaustic requires a ventilation fan to pull out wax vapors. Ventilation can be achieved with a window fan facing outward; however, a hood or industrial exhaust fan would be ideal. Cross ventilation is also important to replace the air going out. The work space should be placed between you and the exhaust; important so that vapors do not pass your breathing zone while on their way out.
Lets talk about fire safety- In the rare occasion of a fire, do not pour water on beeswax; wax explodes when in contact with water and this will cause the flames to spread; simply keep a fire extinguisher handy.
Your work area should have the electrical capacity for use of hotplates and heat guns. Only use heavy duty extension cords and power strips; a quality power strip will shut off if overloaded. Fire can result from overloaded circuits or faulty socket and cords. Exposed wiring can collect wax which will result in fire issues and putting off harmful vapors. Your work area should also be free of solvents and papers- anything flammable.
Experience will give you the tools you need in working with encaustic; in the meantime, check your area often, and keep a first aid kit on hand.
Here are a few links to help get you started + down below.