UPDATE OCT. 25, 2018: Hurricane Willa did not affect Puerto Vallarta, the city experienced a bit more rain than normal and strong waves along the sea edge, but in general the town and bay area was very little affected by this strong weather event.
Puerto Vallarta really has no hurricane season per se, this is because of its location in the middle of the Banderas Bay that is also surrounded on all sides by mountains, sometimes hurricanes pass through the area and the city is a bit affected by them, but mostly on the sidelines. Now, that doesn't mean that PV is in some way magically free from hurricanes, as some liked to believe.
Hurricane Kenna did a lot to eliminate the local legend that the town was always protected from hurricanes by the Banderas Bay. On October 25, 2002, a category 5 hurricane that later made landfall close to San Blas in the neighboring state of Nayarit, let its angry storm surge fall upon Puerto Vallarta.
Strong rain, with winds up to 140 miles per hour (225km/h), and huge waves up to 20 feet tall, battered the Malecon and the city coast.
Luckily no deaths were reported in PV though some 40 people were injured and damage ran up to around 10 million dollars. Three important hotels were severely damaged, many restaurants and shops along the malecon and the Los Muertos beach, including the historical restaurants, La Palapa and El Dorado, were seriously affected by the Kenna hurricane.
The arches in downtown Vallarta were swept away, as were a few of the statues on the boardwalk. The malecon was very damaged and this natural event was used as an excuse to improve the rebuilt malecon/boardwalk.
Another serious hurricane that affected the local population, was Hurricane Lily at the end of August 1971, a category 1 hurricane that made landfall south of Puerto Vallarta, it brought so much rain that the Cuale River flooded the Cuale River Island area, the land there and around it had water up to 8 feet (2.4 m) deep and the people there had to be moved inland.
As stated, previously many believed that the harbor town was in some way geographically protected from hurricanes. Yes, the bay does help a bit, but history has shown it can also fall victim from time to time to some of them, and it's important to remember this so both citizens and local authorities don't become sloppy and reckless.
A prior event is recounted in Mrs. Josefina Cortés de Torres' book "Recordando un Paraíso" (Remembering Paradise), where she writes of a hurricane that hit the city on October 24, 1925. Most of the palapa houses were destroyed, the adobe houses were left without their tile roofs, the kiosk on the plaza was destroyed and the front part of the Saucedo Theater, that had just been built, was destroyed too.
In any case, one thing is quite clear, Puerto Vallarta is not a place where you need to worry too much about hurricanes, if you compare it with Cancun, then PV is a walk in the park, Quintana Roo (the state where Cancun is located) has close brushes and direct hits almost every year. The average for direct hits on Cancun, for example, is one every 7 years (ref: HurricaneCity). Vallarta is more like once every 35 or so years :-).
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