Writing in the Times on Wednesday, Chief Executive Nigel Harris said the UK must be prepared to sacrifice financial gain for global stability.
Referencing an earlier comment in the paper that said "Our values matter more than deals with Saudis", he said: "As a world leader in humanitarian aid, the UK must ensure its policies and practices to protect civilians are consistent.
"The judgement does not change the fact that millions of innocent civilians are being caught up in the fighting and are facing shortages."
The court rejected campaigners' claims ministers were acting illegally by not suspending weapon sales to the kingdom, which is fighting a war in Yemen.
The case was brought by Campaign Against Arms Trade, which said British jets and bombs are being used by Saudi Arabia in its conflict in Yemen, which has led to thousands of civilian deaths. The group said this was done in violation of international humanitarian law and an appeal against the ruling was planned.
Lord Justice Burnett and Mr Justice Haddon-Cave, sitting in London, said the decision to carry on the arms trade was not unlawful.
The judges said "closed material", which had not been made public for national security reasons, "provides valuable additional support for the conclusion that the decisions taken by the secretary of state not to suspend or cancel arms sales to Saudi Arabia were rational".
Equipment sold to Saudi Arabia includes Typhoon and Tornado fighter jets, as well as precision-guided bombs.
Harris urged the UK government to "focus on ensuring that essential supplies can get through to those in need".
He added: "Most importantly, every diplomatic effort must be used to press for a political solution in Yemen."
