In an equation, the quantities on both sides of the equal sign are equal. That's the mathematical meaning of equation, but equation can also be used in any number of situations, challenges, or efforts to solve a problem.
The "equa" at the beginning of equation will be familiar from other words such as "equal," "equality," and "equate." All of these words have to do with making things balance out. An equation is a statement of the equality of two quantities. If that equation is not a mathematical one but rather, say, an interpersonal one, it's still a situation in which you might try to make the two sides equal. For example, taking marriage out of the equation might make it easier for two people to decide to stay together for a while.