Tokyo is a city everyone should see, but it’s also quite a challenge.

For the dazed and jet-lagged first-timer, nothing makes sense – the language, the blinking neon signs, the terrifying public-transport system. By the time you’ve found your feet and stopped wanting to eat dinner at 4am, it’s time to go home.

Which is why you need Charlie Spreckley, a young British expat who gave up his job editing Metropolis, an English-language listings magazine, to found Bespoke Tokyo, a company that offers “urban safaris” – a guided meander around the hidden city of hip bars, secret restaurants and tucked-away teahouses that you’d have no hope of finding bleary-eyed and alone.

Spreckley meets me in the vast lobby of my hotel and leads me through rush-hour crowds to a boisterous backstreet bar in Shinbashi, which resembles a railway carriage with briefcases neatly stashed in overhead luggage racks. Surrounded by black suits, we chew on pig’s ears and drink Sapporo as the staff eye us curiously.

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“This is a classic Shinbashi standing bar. It’s where salarymen come to unwind after a hard day at the office,” Spreckley explains. “This is a difficult city to get to grips with, and it doesn’t help that Japanese people don’t like large, intimidating bars or restaurants. They like small, intimate places and those are hard to find.”

We take a cross-town train to Shinjuku, a vast city within a city. We stroll through the red-light district of Kabukicho, with its sex shops, love hotels, noisy pachinko halls and telephone bars, where lonely men can sit in a booth and phone girls for a “date”. Colourful posters advertise “host bars”, in which wealthy women pay through the nose to be served drinks by chaps who all appear to have modelled themselves on David Beckham.

After 10 minutes, we emerge into Golden Gai, a maze of darkened alleyways that retains the feel of prewar Tokyo. We drink throat-searing shochu at a low-lit bar with room for just four customers. The friendly barman, a singer in a local rock band, serves tofu snacks and plays us his latest CD. Then, on a bamboo-lined path, we duck into Cha Cha Hana (00 81 3-5292 2933), one of a new breed of izakayas (restaurants) pulling in a discerning young crowd. Sitting barefoot on tatami mats, we feast on abalone sashimi and deep-fried pumpkin. It’s tremendous value: dinner for two with drinks costs less than £30.

Eating is one of the great pleasures of visiting Japan. City overcrowding has combined with long working hours and lengthy commutes to create a culture of dining out. Some office workers eat out three times a day, and there is reckoned to be one restaurant for every 16 Tokyoites. One of the latest food fashions is Italian – not big bowls of pasta, but tiny morsels, as served at Sin (6419 3838, www.sin-tokyo.com), a brightly lit basement in the hip shopping district of Omotesando.

Unusually for Tokyo, it also has a reasonably priced (Italian) wine list.

Kita Aoyama Salon, in Gaienmae, is one of Tokyo’s most fashionable and secretive late-night bars. Behind an unmarked steel door (you take exit 2 out of Gaienmae metro station, then turn right) is a stone staircase that leads down into a dark, candlelit basement. It looks like a cross between a Moroccan brothel and a torture chamber. Make yourself at home in a leather armchair, order a champagne cocktail and settle in.

EXPLORING BY DAY appears to be easier. Most tourists start in Ginza, a cross between Bond Street and Blade Runner. On the main drag, Chuo Dori, you shouldn’t have any difficulty finding two of Tokyo’s largest department stores, Mitsukoshi and Matsuya, both of which have basement food halls that make Harrods look like Woolworths. The astonishing array includes just-cooked tempura, sweets the colour of snooker balls and free samples of paper-thin fish crackers.

Even here, however, there are hidden depths. Spreckley leads me down a backstreet beside the all-black Armani building to Cha Ginza (3571 1211), a contemporary version of the traditional Japanese teahouse. We buy tickets (£2.30) at the counter downstairs, then climb up to a minimalist glass and wood room where, seated on a bench, we are served warm sake, two types of green tea and wagashi, a sweet vanilla cake wrapped in foil and crepe paper.

Nearby, in Marunouchi, workers are pouring out of the Tokyo International Forum, a space-age art and convention centre, to eat lunch served from the backs of small vans – Vietnamese noodles, Pakistani curries and Spanish paella. “It’s a modern version of traditional Japanese street-food trolleys,” Spreckley says. “The food’s great and really cheap.”

Next stop is Shibuya, the fizzing epicentre of Tokyo’s pop culture and home to one of the world’s busiest railway stations: more than 2m people pass through daily. Spreckley takes me to his favourite shops, including the 109 Department Store, where Paris Hilton and Gwen Stefani snap up street fashions; Chimera Luxe (www.chimeraluxe.com), which stocks cult Japanese designer labels such as Foot the Coacher and Digital Diverse; and A Bathing Ape (www.bape.com), where, beneath a glass floor, the latest trainers glide by on conveyor belts.

We walk from Shibuya back to Omotesando, cutting down backstreets to find design shops and boutique fashion houses. Spreckley takes me to Loveless (3401 2301), which he declares “the coolest shop in Tokyo”. Handy if you’re after a bronze lamé suit or a £100 pair of pink sunglasses. Sorry, girls, that’s the menswear.

Directly across the street is the more obviously appealing Prada building, designed by Herzog and de Meuron and constructed with dozens of huge, lozenge-shaped glass panels, each said to have cost £50,000. We take the cream-carpeted lift to the top floor and gaze out across the rooftops. “Beautiful,” Spreckley sighs, though I’m not sure whether he means the views or the shoes.

Travel details: Mark Hodson travelled as a guest of Cox & Kings (020 7873 5000, www.coxandkings.co.uk), which has five nights, B&B, at the Peninsula Hotel from £1,695pp and five nights, B&B, at the Shiba Park Hotel for £995pp. Prices include British Airways flights from Heathrow to Tokyo. Or try Inside Japan Tours (0870 120 5600, www.insidejapantours.com), or Japan Travel Centre (020 7255 8283, www.japantravel.co.uk).

Urban safaris with Bespoke Tokyo (www.bespoketokyo.jp) start at £45 per hour for up to three people.

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