The 2016-17 season started first. Their first match was on November 6, the first held in the earliest part of November, where the club defeated ADESBA 3-0. .[3] Three draws were followed, first to Sporting Praia then two scoreless draws first to Celtic Praia then Benfica.[4] The club went on a four match winning streak, Mascarenhas Cabral scored their next goal in three weeks and the club defeated Desportivo 2-1, Vitória 1-2 on December 16 which was their last match of the year, Boavista 1-0 and Garridos 2-3.[5] On January 22, another scoreless draw was made with Tchadense[6] and then the club's first loss of the season was to Travadores 0-1 on January 29 which was their only home loss and their position dropped to third. The club won the next two matches, first to Eugénio Lima then to ADESBA (or Bairro) where they made a comeback after they lost a cup match in the penalty shootouts, their position dropped to fourth, also they scored their next goal in three rounds.[7] A scoreless draw with Sporting was made on February 17. Two more wins were made first to Celtic on February 25 and its goal totals exceeded Tchadense's, then to Benfica on March 5, the latter had the club came back third, goal totals were tied with ADESBA numbering 19, Mascarenhas Cabral scored all the goals in the match, fifth in the regionals, behind Travadores and ahead of Tchadense.[8] Académica lost a position a week later after a loss to Desportivo which was the club's second in the season and was the first of two away, also lost their chance of being regional champion, but surpassed ADESBA's goal's totals by two. Académica made the season's 10th win after defeating the ailing Vitória who slimed their chance of fully remaining in the division and jumped backed to third place and had 35 points, one of the two scorers were Bruno Furtado.[9] Académica suffered a loss to Boavista on March 26 and prevented Académica from returning to second as they did in the ninth round, the club had 23 goals scored, also it was Académica's last loss away to date. Another win was made for the club after defeating the weak Garridos 3-1, a club who was losing the chance to remain in the Premier Division the following season at the time, in the match, two of the three goals were scored by Bruno Furtado.[10] Another draw was made along with Tchadense, this time with three goals and after Desportivo's loss to Sporting, it prevented Académica from becoming third and has a point difference with Desportivo, it also kept their possibility of finishing fourth for the season or no higher than third, fourth they would finish for the season. Bruno Furtado scored one of three goals that match, ranked fifth in the region a three-goal difference with the sixth placed scorer, another scorer was Jacquelino, also the club lost a chance to make a new club record in points. Another win was made on April 23, a week later over Travadores and scored the 30th goal and two additional making it 32, one fewer than Travadores and nine more than ADESBA and had 42 points. The club defeated Eugénio Lima in their final match of the season, Os Garridos' draw did not kicked the club out of the Premier Division, Bruno Furtado was one of the scorers Académica.[11] The club finished fourth with 45 points, the goal totals was 33, a goal difference with Travadores and became two more over ADESBA after their huge win over Travadores. Académica scored 7 home games and lost 2 away games, Most of the goals were scored away while the conceded goals were away while only five were at home.
Académica's 45 points was a club record since their implementation of the three point system in the nation in the mid 1990s. It matched to theirs made in the 2003-04 season. On March 4, 2018, these two records were beaten as Academica had 47 points, exceeding its 45 point total of 2004 and 2017.
Académica appeared in the Santiago South Zone Cup again for the season, this was the first ever challenge with the new club titled Relâmpago, Académica defeated the club 1-0 and kicked the club from further competition in the regional cup. Académica's second match and the last overall of 2016 which took place on December 30, the match went to a goal draw and Eugénio Lima won 4-3 in penalty shootout and Académica went out of the Santiago South Zone Cup.