It is imperative to remember that the Japanese are inherently helpful and friendly people as this politeness is socially taught in the country. Travellers, especially women should never hesitate to ask the locals for help or directions because they are usually more than happy to do so. In fact, some might voluntarily come up to you and try to assist you, expecting nothing in return. I remember how, post my arrival in Tokyo, I was standing outside the train station, going through the otherwise brilliantly illustrated directions to my apartment. I didn't really require any assistance but perhaps the perpetually confused expression on my face prompted an old and extremely elegant lady to abandon her chores and approach me. In an incredibly soothing voice and a rather feeble command over English, she smiled and asked if she could help me. I reciprocated her smile, bowed gently and thanked her and then safely put my faith back in humanity.
Yet another wonderful aspect of Japan is the non-parochial and non-judgemental attitude of the people despite their conservative beginnings. Women travelling and spending time alone in public spaces aren't questioned or looked down upon. Unlike countries like India where a lone woman is often viewed as an invitation, the Japanese understand the concept of privacy and independence for all sexes and genders. You can read to your heart's content while dining alone in a restaurant. You can have your earphones plugged in and shut yourself out from the world in a crowded subway. You can stroll down the streets on a rainy evening and be blinded by the neon lights, a cup of matcha tea resting between your palms. No questions will be asked and no unsolicited judgement whatsoever will be passed.
However, having said that, the other side of the coin can sometimes be dark and tainted. Certain areas of cities like Tokyo are best avoided at night, for example Roppongi, one of the most popular neighbourhoods in the city morphs into its seedy underbelly after dark and is one place where you wouldn't want to be. Moreover, Kabukicho, the red light district of the capital can be quite shady for solo female travellers and so can Kamagasaki, Japan's largest slum in Osaka. While the concept of 'safe spaces' is often questionable and subjective, being cautious isn't really harmful.
Easily the most intimidating aspect of Japan is its language and the fact that English is often not widely spoken in the country. If, like most other travellers, you are unfamiliar with Japanese, make sure that you have adequate essentials to break the language barrier and make your travels smoother. Ask your hotel staff to provide you with maps in English because Google Maps can turn out to be a rather alien and convoluted maze in Japan. Ensure that you have a pocket WiFi with you while going around and install reliable translator apps on your phone or carry phrasebooks if you're old school. Having pictures of everyday signs and necessities can also come in handy because the locals will almost never refuse to point you to the right place. However, do keep in mind that knowing a few greetings and basic words in Japanese goes a long way.