Sam Wright snatched a late equaliser for Kevin Keen's younger team, but Darren Blewitt's strike in the under-19s match wasn't enough against the Robins.
For the second week running, Kevin Keen fielded an under-17 side consisting mainly of schoolboy players, with just two first-year Academy scholars in the starting line-up, and once again the youngsters gave an excellent performance to come from behind and snatch a deserved point.
In a fairly even first half, Hammers had made the brighter start but went a goal down after 25 minutes when the Gunners nicked a scrappy opener following a goalmouth scramble.
The hosts enjoyed the better of the chances in the closing stages of the half, with Ollie Allen going close on two occasions, but Arsenal took their lead into the interval and must have been confident of holding on for three points against their more inexperienced rivals.
The second half turned into a fiercely competitive affair with both sides showing full commitment and excellent work-rate, and it was Hammers who snatched the equaliser they deserved with 15 minutes remaining, when a long free-kick forward was dropped by the keeper at the feet of Sam Wright, who gratefully accepted the gift and tapped home.
Hammers attempted to push on and find a winner in the closing stages, but with Arsenal so dangerous on the break, it was more a case of staying solid and holding on for a hard-earned point.
Said Kevin Keen afterwards: "Once again it was an excellent performance from a very young side and a point was the least we deserved.
"Arsenal have a very good side, with lots of pace and attacking flair as you would expect, but we matched them for most of the game and more than held our own.
"Ollie Allen had a couple of very good chances after they had opened the scoring, but our heads didn't go down and we battled hard for the equaliser in the second half.
"The spirit within this young group is excellent and plays a big part in what they do on the pitch. It's very promising for the future when you can play nine schoolboys in an under-17 match and watch them perform so well."
Team: Reed, Wright, Henry, Norval, White Cohen, Tucker, Shaw (Yao 75), Ephrain, Stokes (Lee 55), Allen (Collington 55). Subs unused: Welsh, Behcet.
Meanwhile, a disappointing week for Tony Carr's older team was rounded off with a painful 2-1 defeat at Bristol City.
Following Tuesday night's disappointing FA Youth Cup quarter-final defeat at Manchester City, Hammers lost out to the Robins in a game that should have provided nothing less than three points.
City took the lead with their first real attack of the first half, when Darren Blewitt's reckless challenge in the penalty area was spotted by the referee and goalkeeper Glenn Jackson was beaten by the resulting spot-kick.
Hammers had an immediate chance to equalise when Danny Morris pulled the ball across the face of the goal for Danny Bunce to convert a simple tap-in, but the young midfielder somehow poked his shot wide when it seemed easier to score.
That set the tone for an extremely frustrating afternoon, and Bristol City doubled their advantage early in the second half when a deflected cross was headed in at the far post.
Darren Blewitt atoned for his earlier error by pulling one back with 20 minutes remaining when he followed up Elliott Ward's shot, but despite throwing everything at their opponents for the rest of the game, Hammers just couldn't muster an equaliser and went home empty-handed.
Said Tony Carr afterwards: "It was a game we should never have lost and I feel like a tape recorder having said that quite a few times recently!
"We had so many efforts on goal - it was like the Alamo in the last 20 minutes - but we just couldn't put the ball in the net. We were mis-timing headers, firing shots wide, and we only had ourselves to blame in the end.
"The two goals we conceded were poor and Danny Bunce's miss just about summed the game up for us. It hasn't been a good week and things are a little bit difficult for us at the moment.
"We are not showing the form of the first half of the season, but that is only to be expected with so many of the players moving up to reserve team football in recent weeks. The side is a lot younger now, but we are still top of the league with a game in hand, so things aren't too bad."
Team: Jackson, McClenahan, Tattam (Ward 46), Laws, Blewitt, Parrington, Bunce, Lumsden (Akinsete 65), Cole, Morris (Pearson 65), Mehmet. Subs unused: Sealey, Fletcher.