The warning was raised on Thursday evening as forecasters anticipate strong south and southwesterly winds will batter the region.
The fresh warning is in force from Friday at 3pm until 8pm, bringing with it a higher danger to life than the previous yellow alert.
Longer journey times and transport cancelations are also more likely as well as power cuts and injuries from debris.
It comes after forecasters issued a yellow warning for rain on Thursday until 10pm before wind gusts of over 70mph are expected when Storm Amy arrives on Friday.
A spokesperson warned some flooding in parts of the country could be expected on Thursday and there may be travel disruption as a result of the conditions.
They added: “Outbreaks of rain are likely at times on Thursday, becoming heavier and more persistent through the afternoon and early evening, before clearing to the east by Thursday night.
“Accumulations of 20-30mm are likely fairly widely, with in excess of 40 mm possible over high ground.
“Given recent wet weather, this may lead to some flooding.
“It will also become rather windy for a time later on Thursday afternoon and into the evening, especially in the east with gusts along the coast potentially in excess of 50mph.”
The Met Office said Storm Amy may lead to disruption across all six counties with the latest warning affecting counties Antrim, Fermanagh, Londonderry and Tyrone.
“Storm Amy is expected to bring a spell of strong winds to Northern Ireland during Friday and Saturday,” they said previously.
“Westerly winds will pick up during the afternoon, peaking during the evening with gusts of 50 to 60mph likely for many areas and could reach 60 to 70mph for a time.
A weather warning has been issued for NI: Pic Andrew McCarroll/Pacemaker Press.
News Catch Up – Wednesday 1 October
“Exposed coasts and hills will see the highest gusts which could exceed 70 mph.”
It comes after a Met Office forecaster said windspeeds of 40mph and heavy rain is expected on Thursday before a short pause on Friday morning.
Heavy rain and stronger winds will resume both inland and on the coast in the evening.
“This is the one that we are a little bit concerned about,” the meteorologist said.
“It’s likely to actually develop and deepen very quickly, so likely to be associated with some strong, very strong and gusty winds.”
Meanwhile, the RNLI has urged the public to safeguard themselves in coastal areas.
The charity advised people to avoid rough seas, cliff edges and exposed waterside areas.
Linda-Gene Byrne, RNLI Water Safety Lead said: “Storm Amy is set to bring potentially dangerous conditions so we’re asking the public to stay vigilant.
“If you plan to visit the coast or a waterside location, we advise that you stay a safe distance from the water as conditions could knock you off your feet or wash you into the sea or water. A visit during weather conditions such as these is not worth risking your life for.”