From Antigua:

Take a shuttle to Chichicastenango (2.hrs 30minutes)
Then take a bus to the terminal in Santa Cruz Del Quiche. From Quiche you can catch a bus to Nebaj (2hrs. 30 minutes).

Or

Take a bus to Chimaltenago(45 minutes) and get off immediately after crossing the Pan-American Highway . Once there switch to a bus headed to Santa Cruz Del Quiche (2hrs 30 minutes) From Quiche you can take a bus direct to Nebaj (2hrs. 30 minutes).

From Guatemala City: City:

Take a bus headed to Chimaltenago (45 minutes). Once there switch to a bus headed to Santa Cruz Del Quiche (2hrs 30 minutes) and from the bus terminal you can take a bus direct to Nebaj (2hrs. 30 minutes).

From Panajachel or Xela:

Take a bus to Los Encuentros. Get off and take a bus to the Santa Cruz Del Quiche terminal (1hr 20 minutes). From there you can take a bus directly to Nebaj (2hrs. 30 minutes).

Additional Info

Buses leave from Santa Cruz Del Quiche to Nebaj sporadically all day until 4pm. The ride up through the mountains is beautiful but not for the faint of heart!

Upon arrival, head to the "Guias Ixiles" Tourism office located next door to "El Descanso" Restaurant just 2 blocks from the Central Park, behind the municipal building, "La Muni".