The scherzo marks a return to the unrelenting march rhythms of the first movement, though in a 'triple-time' metrical context. Its trio (the middle section), marked Altväterisch ('old-fashioned'), is rhythmically irregular (4/8 switching to 3/8 and 3/4) and of a somewhat gentler character. According to Alma Mahler, in this movement Mahler "represented the unrhythmic games of the two little children, tottering in zigzags over the sand". The chronology of its composition suggests otherwise. The movement was composed in the summer of 1903, when Maria Anna (born November 1902) was less than a year old. Anna Justine was born a year later in July 1904. Contemporary interpreters and conductors appear to have accepted Alma Mahler's characterization nevertheless.

Manuscript Movement 3: Scherzo.