Thanks to the production’s use of distinctive, famous, and/or canonical exterior and interior locations, and thanks to various internet sleuths and film buffs (credits and links to be added), we know the filming sites for almost all of the movie’s pivotal and memorable scenes.

Their first day together

• As the movie opens, Jiro is at the window of a watch shop. This
  exterior is Kamine Toa Road Store (カミネ トアロード本店) at 3-1-22
  Sannomiyacho, Chuo Ward, Kobe.
• The stores have changed and the building facade has been remodeled a
  bit, but the iconic scene where she flirts with him as they walk down
  opposite sides of the street was definitely in 浪花町筋 in Kobe,
  specifically in front of “Bar & Bistro 64” at 64番地 Naniwamachi,
  Chuo Ward, Kobe.
• The exterior of the fateful Italian restaurant is Old Kobe Residency
  15th Hall (旧神戸居留地十五番館) at 15 Naniwamachi, Chuo Ward, Kobe.
• The dining room was a set built inside a gymnasium on the campus of
  the Kobe Municipal High School of Science and Technology
  (神戸市立科学技術高等学校) at 1-4-70 Wakinohamacho, Chuo Ward, Kobe.
  It is unclear whether the original gymnasium still stands or if it was
  razed and replaced at some point.

They flee through Chinatown

• Choanmon Gate (長安門) at 1-1-1 Motomachidori, Chuo Ward, Kobe is
  where they enter Chinatown.
• Mitsugi Shoten (三木商店) at 1-3 Sakaemachidōri, Chuo Ward, Kobe is
  where they steal apples.
• One of the distinctive landmarks they run past is Nankinmachi Square
  (南京町広場) at 1-3-6 Motomachidori, Chuo Ward, Kobe.
• They “exit” Chinatown through the main gate of Kuan Ti Miao Temple
  (関帝廟) at 7-3-2 Nakayamatedori, Chuo Ward, Kobe.
• Mikage Public Hall (神戸市立御影公会堂) at 4-4-1 Mikageishimachi,
  Higashinada Ward, Kobe contains the stage where the “Peking Opera”
  was performing, as well as the staircase where the policeman grabs the
  wrong actors.
• Hanadokeisen Street (花時計線通り) across from Daimaru Department
  Store is where they shed their costumes, most recognizably the
  real-world storefront with “Isola Di Motomachi” signage at 3-1
  Sannomiyachō, Chuo Ward, Kobe (seen as Iba Clinic on screen).
• The steps down which the girl leaves Jiro with his eyes closed (the
  same steps at which he sends the cyborg away later) are near Roppongi
  Hills in Tokyo, right next to the Belle Maison Roppongi Towers
  (ベルメゾン六本木タワーズ) which is at 7-20-8 Roppongi, Minato City,
  Tokyo.
• Just before the title card, when we hear Jiro reminiscing about the
  events of that day, we get a glimpse of the huge TV screen on the
  M-INT Kobe building (7-1-1 Kumoidori, Chuo Ward, Kobe) in the
  background. The vantage point is from Sannomiya Station Portliner East
  Entrance, one flight up from street level.

The Cyborg arrives

• The cyborg arrives to her past amid lightning and chaos in the
  intersection at the Akashichosuji Former Settlement Free Walk
  (明石町筋 旧居留地 フリーウォーク) near 47 Akashimachi, Chuo Ward,
  Kobe.
• She battles pickpockets in the alley beside the Minato Bank
  Headquarters building (みなと銀行本店ビル) at 2-1-1 Sannomiyachō, Chuo
  Ward, Kobe.
• She acquires shoes and a new dress at Daimaru Kobe, 40 Akashimachi,
  Chuo Ward, Kobe. Behind the shoe department you can see Caffera which
  is still there today on the first floor.
• HARBS Kobe Clefy Sannomiya Store (HARBS 神戸クレフィ三宮店) at 1-4-3
  Sannomiyacho, Chuo Ward, Kobe is where she enters and points at the
  birthday cake in the display, but when she walks out the door carrying
  it, the scene is at Doutor Coffee, half a block down the same street,
  at 1-3-15 Sannomiyacho, Chuo Ward, Kobe.

Their daily life together

• Jiro’s apartment was a set built inside a gymnasium on the campus of
  the Kobe Municipal High School of Science and Technology
  (神戸市立科学技術高等学校) at 1-4-70 Wakinohamacho, Chuo Ward, Kobe,
  although it is unclear whether the original gymnasium still stands or
  it was replaced at some point.
• In the background of their morning walk is the large stainless steel
  sculpture in Yoyo Square (ヨーヨー広場) at 2-3-1 Minatomirai, Nishi
  Ward in Yokohama, with the vantage point being approximately at Gran
  Mall Park Fountain (グランモール公園 噴水) at 3-4-1 Minatomirai, Nishi
  Ward, Yokohama.
• A few seconds later they arrive at Jiro’s college campus whose
  entrance promenade was filmed at Kwansei Gakuin University adjacent to
  the Main Administration Building at 1 Uegahara 1-banchō, Nishinomiya,
  east of Kobe.
• Real-world Kobe University Rokkodai 2nd Campus (神戸大学
  六甲台第2キャンパス) at 1-1 Rokkodaicho, Nada Ward, Kobe served as
  Jiro’s college when other building exteriors were seen (visually
  unconfirmed). This includes the cafeteria where the girl amusingly
  devours chicken bones, with the distinctive foothills of Mt. Maya and
  the suburbs of Kobe clearly visible outside the windows.
• Classroom scenes were filmed at (unknown).
• The restaurant where the girl gets drunk was filmed at (unknown).
• The interior of Jiro’s part-time job with its mint green walls and
  distinctive chairs seems to be Freshness Burger Sannomiya-chuo-dori
  (フレッシュネスバーガー三宮中央通り) at 1-3-3 Sannomiyacho, Chuo Ward,
  Kobe, although what we see outside the windows does not seem to match
  with reality. It’s possible that they decorated another location to
  look like that particular Freshness Burger branch on the inside.

Jiro’s hometown

The village of Gujo Hachiman in Gifu Prefecture was used as Jiro’s hometown.

• When they get off the bus and look down at the village, the vantage
  point is from the grounds of Gujo Hachiman Castle (郡上八幡城) at
  一の平 659, Hachimancho Yanagimachi, Gujo.
• The festival parade crossing the bridge at dusk is on Miyagase Bridge
  (宮ヶ瀬橋). The procession crosses from real-world south to north into
  the Honmachi neighborhood and the couple is going the opposite
  direction into Shimadani.
• The small red bridge seen in the distance when they greet the
  policeman is Shimizu Bridge (清水橋) at 493 Hachimancho Osakicho,
  Gujo.
• The scenic stream with moss and bridges they walk along is the Otohime
  River near Sakyo Inari Shrine (左京稲荷神社) at 770-1 Hachimancho
  Shimadani.
• The shrine at which they wave to people as they walk by is Hiyoshi
  Shrine (日吉神社) at 683 Hachimancho Shimadani.
• Behind the couple when the little girl shows them the fossils is
  Ishiyama Kimono (石山呉服店) at 828 Hachimancho Shimadani.
• The bus stop where they wait to be picked up after returning to the
  present was filmed at (unknown).

The Cyborg’s jealous rage and other antics

• The courtyard scenes outside Jiro’s rooftop apartment were filmed on
  the roof of the Kobe Center for Overseas Migration and Cultural
  Interaction (海外移住と文化の交流センター) at 3-19-8 Yamamotodori,
  Chuo Ward, Kobe.
• The distinctive building visible from Jiro’s apartment, that the
  cyborg throws an empty can at and hits the Sanyo Bank sign, is the
  Kobe Kanden Building (神戸関電ビル) at 6-2-3 Kanocho, Chuo Ward, Kobe.
• The schoolgirl rescue from the knife-wielding madman was filmed at a
  real school — Takatsuki Minami High School in Osaka
  (大阪府立高槻南高校), which was already closed and vacant at the time
  of filming. The entire campus has since been razed and replaced by a
  residential area and the brand new Shibo Elementary School at 3-30-1
  Shibocho, Takatsuki, Osaka.
• After the disco date, the trio walks to Higashi Yuenchi Park
  (東遊園地公園) at 6-4 Kanocho, Chuo Ward, Kobe. In early 2024 the park
  was bulldozed and rebuilt from scratch, so if you go there now you
  won’t be able to recognize the fountain or any other specific
  locations.
• The earthquake and disaster scenes were filmed in Iwaki City,
  Fukushima Prefecture (いわき市) but the large set was mostly contained
  and no real world elements of Iwaki are recognizable. The only lasting
  evidence is that some local firefighters got their names in the
  credits.

The future

• The grand staircase that the cyborg walks down was filmed in the Gunma
  Prefecture Showa Government Building (群馬県庁 昭和庁舎) at 1-1-1
  Otemachi, Maebashi, Gunma.
• The other interiors of future Jiro’s house — the room with 3 large
  windows, the ballroom, and the dining room — were filmed inside Hyogo
  House (兵庫県公館) at 4-4-1 Shimoyamatedori, Chuo Ward, Kobe