"You Are Not Alone" received positive views from music critics. In more recent years,
Stephen Thomas Erlewine of
AllMusic expressed the opinion that it was amongst some of the best songs Jackson ever released, calling the song seductive. Steve Baltin from
Cash Box described it as a "weepy ballad". In his weekly UK chart commentary in
Dotmusic,
James Masterton said that it "probably ranks as one of the most beautiful songs Michael Jackson has ever recorded". Pan-European magazine
Music & Media wrote, "A far cry from "Scream", Jackson undergoes a gigantic moodswing here. Sad as he is, the vibrato in his vocals perfectly complements the moody ballad". A reviewer from
Music Week rated it five out of five, adding, "Barely a yelp or gulp to be had on this dead simple R Kelly-penned and produced ballad. Not the strongest slowie on the album but a lot of wayward fans will be hankering after some no-frills old style Jackson. A biggie." The R&B critic and journalist
Nelson George described the song as lovely and supple.
Jon Pareles of
The New York Times felt it was the only conventional love song on the new material on
HIStory. He compared it to
Mariah Carey's song "
Hero" and said it "sounds like a surefire hit". James Hunter of
Rolling Stone noted that, "the excellent current single '
Scream' or the first-rate R&B ballad 'You Are Not Alone'—manage to link the incidents of Jackson's recent past to universal concepts, like injustice or isolation. When he bases his music in the bluntness of hip-hop, Jackson sketches funky scenarios denouncing greed, blanket unreliability and false accusation". Writer and journalist
J. Randy Taraborrelli wrote of the song in 2004, "[it] remains among Michael's best songs ... On listening to 'You Are Not Alone', one wonders how many times Michael tried to tell himself, during his most desperate and anguished times, that he
did have support in his life, from a higher power, or even friends and family, whether he actually believed it or not". Fred Shuster of the
Daily News of Los Angeles described it as the best song on the album. Conversely, while Steve Holsey of
Michigan Chronicle gave the album a positive review, he described the song as the worst on the album, calling the Kelly penned lyrics "
trite" and below the standard set by Jackson's own lyrical skills.
Robert Christgau of
Blender would later call it "quietly yucky" while pop music critic Bill Wyman of
New York called it "drony and unpleasant." Revisiting "You Are Not Alone" in 2022, Tom Breihan of
Stereogum negatively described the song as "thin gruel" and as a "sort of generic sad ballad", while complimenting Jackson's vocals for sounding "as tender and reassuring as ever". "You Are Not Alone" received an
American Music Award nomination and a
Grammy nomination both for "Best Pop Vocal Performance". ==Chart performance==