There are sometimes exit fees randomly applied at both borders, typically US$3–5. There shouldn’t actually be an exit fee, but Honduras [1] does have a US$3 reentry fee for those from outside of Central America.
Regular buses depart Nueva Ocotepeque [2] all day to the Guatemalan border at Agua Caliente (22 kilometers, US$1.50). Between the Honduran and Guatemalan border posts is about three kilometers of lonely road—rides are infrequent, so make sure to get to the border by midafternoon at the latest. Travelers arriving from Esquipulas, Guatemala, will find frequent transportation to Nueva Ocotepeque until 6 p.m. daily.
The border reportedly closes at 2 a.m., but it’s best to get there earlier. Taxis from Nueva Ocotepeque charge US$10 (less if you share) and usually go until about 10 p.m. Moneychangers arrive at 9 a.m.; some offer decent rates, while others are happy to rip you off if you don’t know the rates. Beware.
At least six buses daily between 5 a.m. and 6 p.m. drive from the border to San Pedro Sula [3] in six hours (US$7), with stops at Nueva Ocotepeque and Santa Rosa de Copán [4], with Toritos y Copánecos or Empresa Congolón. Toritos y Copánecos also runs several buses a day directly to Tegucigalpa [5], nine hours.
Buses run frequently between Nueva Ocotepeque [2] and El Poy at the Salvadoran border (seven kilometers, US$0.50) until 7 p.m., but consider taking a collective taxi since it’s just US$0.85. Private taxis are about US$6. It’s always best to get to the border early to ensure buses onward. The border itself, not much more than a roadside collection of buildings with a lot of semitrucks lined up waiting to cross, is open daily 6 a.m.–7 p.m.
Links:
[1] http://www.moon.com/destinations/honduras
[2] http://www.moon.com/destinations/honduras/western-honduras/nueva-ocotepeque
[3] http://www.moon.com/destinations/honduras/central-honduras/san-pedro-sula
[4] http://www.moon.com/destinations/honduras/western-honduras/santa-rosa-de-copan
[5] http://www.moon.com/destinations/honduras/southern-honduras/tegucigalpa