Tracking west-northwest as it rounded a subtropical ridge, Flo slowly deepened, and on September 15, became a typhoon.

Shortly thereafter, the typhoon began to recurve to the northeast towards Honshu in response to deepening troughs to the northwest and north of the system, which resulted in a weakening trend due to increased vertical wind shear despite remaining over warm water.

On September 19, Flo made landfall on southern Honshu, becoming the first typhoon to hit the Kii Peninsula in 11 years, and thereafter started to transition into an extratropical cyclone.

For a period of three days, the typhoon dropped heavy rainfall across much of the Japanese archipelago, which inflicted damage in 44 of 47 prefectures.

Across the Amami Islands, 13 people were killed, 29 others were hurt, 917 homes were damaged, and an additional 446 houses were destroyed, resulting in 2,327 homeless individuals.

While damage in Tokyo was slight, 260,000 passengers were stranded after 117 trains along the Tōkaidō Shinkansen line were disrupted.

Due to a prolonged period of heavy rain, partially caused by Flo, rainfall was 300% of normal in some locations on the island as of mid-September 1990 while sunshine time was a mere 64% of average in Hokkaido Prefecture.

[nb 1] The origins of Typhoon Flo can be traced to an area of convection that first formed to the southeast of the Marshall Islands on September 7.

At 06:00 UTC the next day, the Joint Typhoon Warning Center (JTWC) started tracking the system[1] while it was located about 430 km (270 mi) east-southeast of Guam.

Over the next four days, the storm's convective structure slowly improved caused by an expansion of its equatorial outflow channel while also turning westward - on a course typical of a straight runner.

[3][nb 2] Following the disturbance's development of a well-defined upper-level center and an additional increase in organization, aided by the subtropical jet the JTWC issued a Tropical Cyclone Formation Alert at 05:30 UTC that day.

[1] Six hours later, the JMA upgraded the depression into a tropical storm,[3] with the JTWC followed suit based on Dvorak classifications of T2.5/65 km/h (40 mph).

[1] Around this time, Flo began to track west-northwest at a pace of 23 km/h (14 mph) under the influence of a subtropical ridge to the north.

[1] Around this time, the JMA estimated the typhoon peaked in intensity, with winds of 225 km/h (140 mph) and a pressure of 890 mbar (26 inHg).

[3] Around the time Flo peaked in intensity, the typhoon began to recurve to the northeast in response to a deepening mid-latitude shortwave trough to the northwest, which induced a break in the subtropical ridge.

Weakening continued due to increased vertical wind shear, although the warm waters of the Kuroshio Current helped Flo maintain some of its intensity.

Typhoon Flo accelerated northeastward towards Honshu in response to a trough passing north of the system.

[1] At 00:00 UTC on September 20, the JMA declared Flo extratropical,[3] while the JTWC downgraded it to a tropical storm.

[23] For a period of three days,[24] the typhoon dropped heavy rainfall across much of the Japanese archipelago,[25] which caused damage in 44 of 47 prefectures.

[31] In Naha, the capital of Okinawa, strong winds destroyed neon signs, tore away store-front shutters, and tossed bicycles across streets.

[35] On the eastern portion of Shikoku Island, in Tokushima Prefecture, one person fell and died, another was wounded, 852 homes were damaged, and 60 others were destroyed.

[43] The inner core of the typhoon passed over Kyoto Prefecture and lashed the region with high winds for several hours.

[47] Prefecturewide, damage totaled ¥15.9 billion; Flo was the worst tropical cyclone to affect the area since Typhoon Kathy in 1964.

[51] Along the west coast of central Japan, in Toyama Prefecture, heavy rains caused 107 landslides while rough seas damaged nine ships.

Most of Tochigi Prefecture received heavy rains, which caused damage to 30 homes, 70 embankments, and two bridges.

[57] Additionally, 20 homes were flooded and 3,000 households lost power along coastal areas of Saitama Prefecture.

[60] In Yamanashi Prefecture, one person was hurt and one hundred ten homes were damaged or destroyed, which resulted in 419 people homeless.

[69] Late on September 19, the typhoon passed directly over Iwate Prefecture, where there were reports of 32 landslides, 1 fatality, and 275 flooded houses.

[19] Elsewhere, in Fukushima Prefecture, 1,300 people lost power due to strong winds, and damage to crops totaled ¥143 million.

Due to a prolonged period of heavy rain caused by Flo, in conjunction with several other tropical cyclones, rainfall was 300% of normal in some locations on the island as of mid-September 1990 while sunshine time was a mere 64% of average.