Fish oil can be taken at any time of the day. However, studies have stated that taking them with meals helps them absorb better in the body especially a high-fat meal. Research has also observed that the potential benefits of fish oil supplements are not immediate but long term, therefore timing is of no particular importance. However, if you can split your servings into two smaller doses, that is in the morning and in the night, it can help you with gastrointestinal problems such as acid reflux.