At a general level, they are synonymous, both meaning ‘a distinct religious group or movement’ or ‘an autonomous Christian Church’, with ‘sect’ having a somewhat more negative connotation
A denomination is indeed an autonomous Christian church or community, particularly of the Protestant movement. Not just the general families/communions (Anglican, Lutheran, Methodist, Baptist), but the specific autonomous churches (Church of England, Evangelical Lutheran Church in America, United Methodist, Southern Baptist). Thus one could say that there are several Lutheran or Baptist denominations.
Denominationalism represents, some would say, a moral and ecclesiological failure in the church, legitimate diversity pushed and exaggerated to the point of division, contrary to the nature of the Church of Christ as a united and universal fellowship in faith.
A sect, traditionally, is a schismatic group that deviates from the accepted, mainstream, or orthodox position.
More commonly, today, it emphasizes more of a sociological than a theological distinction - sects emphasize separation, isolation, exclusivist worldview, and tend to follow a personality. Denominations/churches, on the other hand, are more universalizing, integrative, inclusivist, and institutional.
At the same time a sect is distinct from a cult in that it has a prior tie to a church or denomination, and then spun off on its own, whereas a cult tends to grow up ‘ex nihilo’ as it were: pure creative (or manipulative) genius and charisma.
So, one might speak of ‘Catholic sects’ - not the Catholic Church, but splinter groups therefrom, like the Society of Pius X, Society of Pius V, or the “True Catholic Church” and other sedevecantist movements.
Sometimes a sect can grow into a church - the Church of Latter-Day Saints, Adventists, even Salvation Army started more like sects and have developed into denominations or churches.
Sectarianism represents the temptation to see one’s own church or denomination as defined in opposition to the other - emphasizing often minor practices or characteristics simply because they are different that someone else. This is also a moral and ecclesiological failure.
NB: Though it might have been seen as a series of sects, anachronistically, in the 16th century, the Protestant churches and communities would not be considered ‘sects’ by the Catholic Church today.