They probably don't realise why, but it is largely because the red sun is an omnipresent national symbol, appearing on the Rising Sun flag. In isolation, such cultural differences are not important - until a child from one culture is transferred to another.
Children tend to have fairly fixed views on things like the colour of the sun, as they do on the fair distribution of dessert helpings or the rules for hide and seek. So for a child who has been brought up painting the sun red to be confronted with others who paint the sun yellow, the experience is likely to be unsettling, to say the least.
But for Yoshiko Otsuka, a counsellor in Tokyo who helps Japanese children prepare for a stint abroad, the sun's colour disparity is something that can be turned around to help her young charges adapt to European or American life.
'I say to them: 'Hey, isn't that interesting?' and try to let them see it is not wrong, but just different, and that it is OK to be different,' she says.
Learning that it is 'OK to be different' is a particular novelty in Japan, where schools go out of their way to press everyone into the same mould.
Conforming, learning by rote, and adhering to the group are promoted as virtues.
'Japanese culture tries to persuade us we are all the same. But it is just not true,' said Ms Otsuka, who has a masters degree in counselling from Columbia University in New York.
Ms Otsuka set up the Intercultural Counselling Institute in Tokyo in 1986, and since then has been running courses for children whose families are being transferred overseas - usually because of the father's work. As the number of overseas subsidiaries of Japanese corporations has increased over the past decade, so too has the number of Japanese living overseas.
Some 660,000 Japanese citizens live outside the country, according to the Foreign Ministry. And whereas in the past fathers would often go overseas on their own, leaving their children and wives in Japan, these days more and more families are travelling together.
Expatriate life is fraught with problems and potentially embarrassing situations. For the parents, the principal fear concerns language, since the teaching of spoken English or other foreign languages is notoriously poor in Japan. But for children the means of communication is less worrying.
'The main fear of most of the children I work with is whether they will be able to make friends in the foreign country,' said Ms Otsuka. 'Compared to their parents, their concerns are very positive.'
Ms Otsuka holds three two- hour sessions with the children before they leave Japan, during which she tries to give them a few ideas on starting a new life in a foreign country.
At the first session, for example, she pairs the children off - most are strangers to each other - and tells them to get to know each other. But they are not allowed to speak. There are a variety of toys, ropes, blackboards and paper cut-outs in the room, which the children can use. After some time, Ms Otsuka sits everyone down and gets them to relate their experiences.
'A typical response might be: 'I gave her a paper cut-out, she smiled, and we became friends'.' Ms Otsuka says. 'I use the fact that they are strangers among themselves, and when it is all over, I tell them this was a practice, and how much easier it will be when they try it again after going abroad.'
The older the children, the more difficult it is to get them to open up. At kindergarten level, everyone just plays together, with no concern for race or language. From the age of 11 or 12 onwards, self-consciousness begins to develop, and the children are afraid of losing face.
'It is difficult to make mistakes at that age,' says Ms Otsuka with a smile.
But often the most intractable problems are the fears of the parents, which the children simply reflect in their own behaviour.
'We Japanese are brought up not to speak freely in front of other people,' Ms Otsuka says. 'Often when mothers come to me to discuss their children's fears of going overseas, in fact, they are talking about themselves.'
Adults, it seems, find it even harder to accept that the sun can be either yellow or red.