A 79-year-old man who once supervised altar boys as a layman in a Dorchester parish was arraigned Wednesday on charges that he raped a boy that he met nearly 30 years ago through his local church and youth baseball.

Michael Walsh, who was ordained as a priest in Michigan in 2002 but quickly stripped of his ministerial duties because of a separate complaint, pleaded not guilty to two counts of child rape and three counts of indecent assault and battery on a child under age 14.

During Walsh’s arraignment in Suffolk Superior Court, a prosecutor alleged he attacked the boy, assaulting the child in his car, at his home in Dorchester, and in his office between September 1988 and June 1991.

The alleged victim, who is now 38 years old, came forward in June and disclosed that he had been abused by Walsh as a child, authorities said. A grand jury indicted Walsh Sept. 16, the Suffolk district attorney’s office said.

Suffolk Assistant District Attorney Ashley Polin said Walsh used his role at St. Brendan Parish and his coaching position with the Cedar Grove Baseball League to “gain access to, groom, and ultimately sexually assault the victim.’’

She said the child was attacked from the time he was in fourth grade until he was in sixth grade at St. Brendan School in Dorchester.

Walsh frequently took the boy he’s now accused of attacking and other children to restaurants, movies, and weekend trips, driving them to different places and then dropping them off at home, Polin said. The boy was also attacked at a hotel during a youth baseball trip to Cooperstown, N.Y., she said.

“The victim in this particular case was always the last child to be dropped off because he lived the closest geographically to the defendant,’’ Polin said.

Walsh and his lawyer, Matthew Thompson, declined to comment as they left the courtroom. Walsh is due back in court Nov. 14.

Prosecutors said they brought charges against Walsh under changes in the law made in 2006 that eliminated the statute of limitations in child sexual abuse cases and replaced it with a requirement that authorities have “objective, corroborative evidence’’ if the alleged abuse happened more than 27 years ago.

“Changes in the statute of limitations law for child sexual abuse cases help us, but it means nothing without the bravery of abuse survivors who overcome their fear and shame to disclose trauma,’’ Suffolk District Attorney Daniel F. Conley said in a statement.

“Survivors, young or old, should know that they can always count on us to help, support, and speak for them,’’ Conley said.

Polin said Walsh grew up in Charlestown and served as head altar boy at St. Francis de Sales Church during the mid-to-late 1950s. He then joined the United States Air Force before moving to Dorchester in the 1980s, she said.

In the mid-1990s, Polin said Walsh retired to Florida and then moved to Maryland to study for the priesthood.

He was ordained as a priest on June 1, 2002, in Grand Rapids, Mich., but was relieved of his priestly duties just a month later after allegations of sexual abuse surfaced from Walsh’s time at St. Francis de Sales Church in Charlestown, Polin said.

She said Walsh, who lives in Pembroke, has also faced civil action over similar accusations.

Church officials in Grand Rapids took action against Walsh before he was to start his first assignment as a priest, said Annalise Laumeyer, spokeswoman for the Roman Catholic Diocese of Grand Rapids.

The Roman Catholic Archdiocese of Boston declined to comment on Walsh but urged anyone interested in reporting sexual abuse by the clergy, a church employee, or a volunteer to contact its Office of Pastoral Support and Outreach.

Laura Crimaldi can be reached at laura.crimaldi@globe.com. Follow her on Twitter @lauracrimaldi.