Getting from Xela to Nebaj by chicken bus is super easy. Don't get me wrong, its a long day, but its easy and the scenery is spectacular.
We took the minibus (Q1.25pp) from near Parque Central to the Mall (Pradera) instead of the actual terminal stop. It is 2 stops later on the same route. You'll get out by a Pollo Campenaro and a Pizza Hut. The terminal (aka bus parking lot) is straight down the street to your right. We liked this option better because it saved us walking through the busy market with our bags. Why the 'terminal' stop is a large obstacle away from the actual terminal makes absolutely no sense. But, then again, many things in Guatemala make little sense.
From Xela we took a bus to Santa Cruz del Quiche (called just Quiche by most). It was easy to find the right bus in Xela by just asking people that were standing near buses. They'll always point you in the right direction. Our bus left at 9am. It took about 2.5 hours to get to Quiche (Q25pp).
From Quiche there were direct buses to Nebaj. Both of the big and minibus variety. The connection time was pleasantly short and that bus took about 2.5 hours as well. (Q 20pp).
We left Xela at 9am and were in Nebaj just after 2pm. So it was just over 5 hours, not including the minivan from Central Xela. We recommend grabbing a delicious bagel (Cheddar Pimento was our favourite) and maybe a cookie or two for the journey! They open at 6am for your convenience.
We referenced this helpful blog before we went: