Asked as someone learning Japanese. Findings drawn from Japanese-specific research are framed for Japanese learners and may not hold for other languages; where the evidence is general second-language research, the report says so.
The sources here don't contain a systematic side-by-side grammar comparison of English and Japanese, but several studies that specifically test English speakers learning Japanese (and Japanese speakers learning English) converge on a few clear structural differences: word order (Japanese verb-final vs. English subject-verb-object), the use of case-marking particles instead of fixed word order, and freedom to rearrange ("scramble") sentence elements in ways English can't. These differences show up as concrete learning difficulties, especially in how learners process sentences in real time.
Japanese places the verb at the very end of the clause, while English places it in the middle (subject-verb-object). Because of this, native Japanese speakers can't rely on the verb early in a sentence to predict how the sentence will unfold the way English speakers do — instead they rely heavily on grammatical particles attached to nouns.1,5
Japanese marks 'who did what to whom' with small particles attached after nouns (case markers), rather than relying on fixed word order the way English does. This lets Japanese speakers move words around in a sentence far more freely than English allows, a phenomenon called 'scrambling.'1,5,7
In plain terms
Example
Across many of the world's languages, there's a general pattern where languages with flexible word order (like Japanese) tend to also have case marking, while languages with fixed word order (like English) tend not to need it — and experiments show that learners naturally start using more case marking when a made-up language allows flexible order.3,7
When native English speakers learn Japanese, they can eventually process reordered ('scrambled') Japanese sentences without extra difficulty, similar to native Japanese speakers, but this ability tends to depend on their proficiency level. Errors in producing the reordered structure are often linked to a lack of grammatical knowledge and to defaulting back to the standard subject-object-verb order they know from English.5
A dissertation focused specifically on English-speaking learners of Japanese found that when learners misproduce reordered ('scrambled') Japanese sentences, it's often because they fall back on the standard Subject-Object-Verb template instead of correctly rearranging elements — but this fallback effect appeared mainly with sentences where both the subject and object could plausibly be either one (i.e., both are animate/human-like), not in sentences where only one reading made logical sense.5
Example
Among English-speaking learners of Japanese, the more advanced ones used the case-marking particles more consistently and reliably during sentence comprehension than less advanced learners, suggesting that mastering this particle-based system is a gradual process rather than something picked up all at once.5
Japanese and English differ in how they describe the 'manner' of movement (e.g., how something moves, not just that it moves) in both speech and accompanying hand gestures. When native Japanese speakers become intermediate learners of English, this difference doesn't just show up as language influencing their English — their English also starts to influence how they express manner even when speaking Japanese.2
In plain terms
A broad typological comparison of verb 'aspect' systems (how a language marks whether an action is ongoing, completed, repeated, etc.) across 16 languages found that Japanese has an aspect system that doesn't fit neatly into either of the two most common patterns worldwide, one of which is the pattern English uses (progressive vs. non-progressive, e.g., 'is running' vs. 'runs').4
In plain terms
A study of learners of English from several native-language backgrounds, including Japanese, found that adult second-language learners tend not to fully track certain grammatical dependencies across long stretches of a sentence (e.g., connecting a question word to a distant verb) the way native speakers do — a pattern seen even in Japanese-speaking learners of English, whose own native grammar handles this differently.6
Because Japanese relies on particles attached to words rather than word order to signal grammatical roles, it's worth deliberately practicing noticing and producing those particles rather than assuming word order alone will convey meaning as it does in English — sentence mining real examples of reordered ('scrambled') sentences and drilling particle use through targeted grammar study can help. Given that learners' handling of reordered Japanese sentences improves with proficiency and explicit grammatical knowledge (rather than emerging automatically), structured grammar lessons that explicitly teach the particle system and scrambling patterns, paired with reading or listening practice that exposes you to naturally-occurring reordered sentences, are likely to speed up this part of acquisition. Since English word-order habits (like defaulting to Subject-Object-Verb) can intrude into Japanese production, conscious practice producing non-default word orders — for example through writing practice or sentence-construction drills — may help override that default.