There are mainly two border crossing points between Mexico and Guatemala, both through the state of Chiapas in Mexico. It is mostly the same principal traveling from Guatemala to Mexico.
It is important to know that each border gives access to a specific part of Guatemala and you should choose which border to cross depending on where you are going, either towards Tikal and Flores or towards Antigua and Panajachel.
The border from Palenque gives you access to the eastern part and Flores / Tikal region of Guatemala. This border crossing point is located at the Mayan ruins of Yaxchilan and Bonampak. The cost from Palenque to Flores is about us$35 per person (about 7 hour ride) and runs daily. Almost all the tour operators in the town of Palenque can sell you the tickets.
You are basically picked up at your hotel around 6:30am in a van that will take you to Yaxchilan and Bonampak ruins sitting on the Usumacinta river which is the natural border between Mexico and Guatemala. There you will need to process out of Mexico. Make sure to have your green Mexican visa card (which you received at the airport when you first arrived) along with your passport handy. You will also be asked to pay a fee of about us$30.
Once everyone is processed out of Mexico you will take a short 200 meters (600 feet) walk to the river where a boat will be waiting for you. The boat ride lasts about 15 minutes going up the river to the Guatemalan border where a van will be waiting for you.
By law there are no entry or exit fees into Guatemala but the border patrol may charge you anywhere between us$1 to us$7 dollars to enter the country. A way for them to make some money on the side for themselves…
Once processed into Guatemala you get back on the van and take a short 2 to 3 hour ride to the beautiful island of Flores on the Peten Itza lake of Guatemala. You will arrive to Flores around 4pm.
If you are coming from Flores, you will find that many of the travel operators on the island offer the same trip from Flores to Palenque for about the same price.
From SAN CRISTOBAL DE LAS CASAS
From San Cristobal de las Casas you have only access to the western part and Antigua/Lake Atitlan region of Guatemala. Here you will also find many tour operators offering this 12 hour trip daily for a cost of about us$40 per person. You will need to choose if you want to go to Antigua or Panajachel.
You are picked up at your hotel around 6:30am with a van and head towards the town of Ciudad Cuauhtemoc in Mexico. The van will make a stop on the Mexican border for everyone to get process out of Mexico before getting back on the bus. Again have your green visa card (received at the airport upon arrival) along with your passport and us$30 exit fee handy.
The van will then drive you to the Guatemalan side (2 kms) of the border, to the town of Mesilla. Here you will have to change vans and get processed into Gautemala. By law there are no entry or exit fees into Guatemala but they may charge you some us$1 to us$5 dollars per person to enter the country.
Once processed into Guatemala you get back on the van and head south towards Antigua or Panajachel depending on your destination. You will get into Antigua or Lake Atitlan around 6pm.
If you are going north towards Mexico you will easily find the same transportation service with the tour operators in Antigua or one of the towns around the Lake Atitlan.