The yellow - “be aware” - alert involves up to 100mm (4in) of rain falling, with strong winds likely to fell trees and blow down leaves, blocking drainage.
The warning extends between Argyll and just south of Ullapool and includes all the Hebrides except the extreme west of Islay.
It will be in force from midnight to 9pm on Saturday.
The Met Office said 50-80mm (2-3in) may fall in a 36-hour period from Friday, with up to 100mm over exposed hills in the north west.
A spokeswoman said: “Across the West Highlands and Western Isles, rain will become persistent later on Friday and occasionally turn heavy during Saturday.
“Rain will be accompanied by strong to gale force southerly winds, and leaf fall and tree debris may reduce road drainage.
“Excess surface water could lead to localised flooding in prone areas, whilst strong winds are also likely to generate rough seas.
“Be aware of the likelihood of some limited travel disruption and difficult driving conditions.
"The rain will start to clear this region later on Saturday evening.”
The spokeswoman said it would be caused by an Atlantic frontal system, with moist air and strong flow combining to produce heavy rainfall, especially over high ground.