Andrew MacLaren has come there  with his two daughters, Fiona and Jean; the latter is soon to be married to Charlie Dalrymple, much to  the displeasure of Harry Beaton, who wants to marry her himself. Meg Brockie, a brash young woman,  expresses surprise that Fiona is not jealous of her sister, since becoming a bride is quite an event and  achievement in Brigadoon. Fiona explains by giving Meg a clue to her personal philosophy ("Waitin' for  My Dearie"). When Jeff and Tommy are observed all the activities in the square stop short, for they are not only strangers but strangers from a distant land. Tommy is immediately attracted to Fiona. When the latter announces she is going to gather heather for her sister's wedding, Tommy insists he be allowed to accompany her. At first Fiona declines, but she grows more amenable after Tommy has sung a plaintive tune to her ("Heather on the Hill"). They now go off, hand in hand.

Later, in the MacLaren home, Jean is preparing to pack in preparation for her imminent wedding. The bridegroom, Charlie, comes to inscribe his name in the MacLaren family album, after which he sings of his intense longing for his bride ("Come to Me, Bend to Me"). Then Fiona and Tommy return from their expedition, late and happy. When Jeff appears, Tommy confides his feelings for Fiona ("Almost Like Being in Love"). Jeff and Tommy come upon the family album. Glancing through it, they remark the peculiar coincidence that a hundred years ago, on this very day, a Fiona MacLaren was married to a Charlie Dalrymple. It is their first clue that something eerie is happening around them. Fiona refuses to enlighten them, so they seek out one of the venerable citizens of Brigadoon, Mr. Lundie, and learn from him of the strange history of this town that lives one day every hundred years.

The wedding ceremony now takes place, with the festive townspeople enjoying songs and dances. Suddenly Harry Beaton arrives, determined to prevent the marriage from taking place. He lunges at the bridegroom with his knife, but, fortunately, Tommy arrests his hand. As Harry flees, Jeff trips him; Harry falls on his head and is instantly killed.

When the wedding is over, Tommy confesses to Fiona he loves her dearly ("There But For You Go I"). Because of Fiona he is determined to stay in Brigadoon, come what may. But Jeff convinces him that it is impossible for Tommy to live in a dream, that reality dictates Tommy must return home to New York and marry his fiancée, Jane Ashton. Sadly, Tommy realizes the wisdom of Jeff's words. He bids Fiona a tender farewell ("From This Day On") and leaves Brigadoon with Jeff.

Back in New York, Jane Ashton upbraids Tommy for having failed to "come to me" as soon as he had returned from Europe. The words "come to me" strike a responsive chord with Tommy. In a mist he sees Fiona before him in Brigadoon. This vision convinces him that he must break with Jane Ashton once and for all. It also convinces him that he must return to Scotland. With Jeff once again as his companion Tommy is back in the forest outside Brigadoon. Somewhere in the mist, whispers Tommy, there is a girl he desperately wants but knows he will never get. Jeff inquires if this is the reason Tommy has made the long journey back to Scotland. Tommy now reveals he simply had to convince himself that Fiona and Brigadoon belong not to the real but to the dream world. Suddenly Tommy hears voices in the distance, and sees Mr. Lundie approaching him. He takes Tommy by the hand to lead him back to Brigadoon. "You see," explains Mr. Lundie, "love can do anything –even miracles." Waving farewell to Jeff, Tommy follows Mr. Lundie into the Highland mists.